diff --git a/.gitignore b/.gitignore index 3fb4a86..53b6cd5 100644 --- a/.gitignore +++ b/.gitignore @@ -4,7 +4,6 @@ .DS_Store semantic.cache bin/ -catalog-v001.xml *.tmp *.tmp.obo diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 378a967..e9c06f9 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -22,6 +22,7 @@ These are the current imports in OGMS | iao | http://purl.obolibrary.org/obo/iao.owl | mirror | | ido | http://purl.obolibrary.org/obo/ido.owl | filter | | omo | http://purl.obolibrary.org/obo/omo.owl | mirror | +| cob | http://purl.obolibrary.org/obo/cob.owl | slme | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index cc5b8f7..cf3cd42 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,7 +16,7 @@ # 3. [Update repo to latest ODK](update_repo) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 04d4c89977807b1ad2521b6386e797df708e1d2805834dc0af9cc669ff68d53d +CONFIG_HASH= 1fc11db5bb385926b27aa9fa890f57825a32f749e19de3b6ec2c22720f272f95 # ---------------------------------------- @@ -194,7 +194,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro obi bfo iao ido omo +IMPORTS = ro obi bfo iao ido omo cob IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -571,6 +571,14 @@ mirror-omo: | $(TMPDIR) $(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl +## ONTOLOGY: cob +.PHONY: mirror-cob +.PRECIOUS: $(MIRRORDIR)/cob.owl +mirror-cob: | $(TMPDIR) + curl -L $(OBOBASE)/cob.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/cob-download.owl -o $(TMPDIR)/$@.owl + + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 16d739d..69c9ccc 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -7,5 +7,6 @@ + \ No newline at end of file diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index ebff232..a44b0bb 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,14 +7,21 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2025-07-02") +Annotation(owl:versionInfo "2026-01-31") Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -26,6 +33,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) ############################ @@ -92,6 +100,14 @@ AnnotationAssertion(rdfs:label "ent AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) AnnotationAssertion(rdfs:label "continuant"@en) SubClassOf( ) +DisjointClasses( ) + +# Class: (occurrent) + +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) # Class: (independent continuant) @@ -108,6 +124,53 @@ AnnotationAssertion( "independent continuant"@en) SubClassOf( ) DisjointClasses( ) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) # Class: (specifically dependent continuant) @@ -124,6 +187,28 @@ AnnotationAssertion( "the smell of this portion of mozzarella"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) # Class: (material entity) diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl new file mode 100644 index 0000000..40acd2d --- /dev/null +++ b/src/ontology/imports/cob_import.owl @@ -0,0 +1,385 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2026-02-10") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion(rdfs:label "definition") + +# Annotation Property: (editor note) + +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (term replaced by) + +AnnotationAssertion(rdfs:label "term replaced by"@en) + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion(rdfs:label "part of"@en) + +# Object Property: (has part) + +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion(rdfs:label "has part"@en) + +# Object Property: (realizes) + +AnnotationAssertion( "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process"@en) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is about) + +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + +# Object Property: (has specified input) + +AnnotationAssertion( "The inverse property of is specified input of") +AnnotationAssertion(rdfs:label "has specified input"@en) +ObjectPropertyDomain( ) + +# Object Property: (has specified output) + +AnnotationAssertion( "The inverse property of is specified output of") +AnnotationAssertion(rdfs:label "has specified output"@en) +ObjectPropertyDomain( ) + +# Object Property: (is specified output of) + +AnnotationAssertion( "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion(rdfs:label "is specified output of"@en) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion(rdfs:label "characteristic of"@en) + +# Object Property: (has characteristic) + +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion(rdfs:label "has characteristic"@en) + +# Object Property: (participates in) + +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion(rdfs:label "participates in"@en) + +# Object Property: (has participant) + +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion(rdfs:label "has participant"@en) + +# Object Property: (is concretized as) + +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) + +# Object Property: (concretizes) + +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) + +# Object Property: (has output) + +AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") +AnnotationAssertion(rdfs:label "has output"@en) + + + +############################ +# Classes +############################ + +# Class: (process) + +AnnotationAssertion(rdfs:label "process"@en) + +# Class: (disposition) + +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) + +# Class: (realizable entity) + +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) + +# Class: (role) + +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) + +# Class: (immaterial entity) + +AnnotationAssertion(rdfs:label "immaterial entity"@en) + +# Class: (proton) + +AnnotationAssertion( "Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.") +AnnotationAssertion(rdfs:label "proton") +SubClassOf( ) + +# Class: (atomic nucleus) + +AnnotationAssertion( "A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.") +AnnotationAssertion( "Some people may be uncomfortable calling every proton an atomic nucleus"@en) +AnnotationAssertion( "This is equivalent to CHEBI:33252"@en) +AnnotationAssertion(rdfs:label "atomic nucleus") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (subatomic particle) + +AnnotationAssertion( "A particle smaller than an atom.") +AnnotationAssertion(rdfs:label "subatomic particle") +SubClassOf( ) +DisjointClasses( ) + +# Class: (cell) + +AnnotationAssertion( "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc."@en) +AnnotationAssertion( "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism."@en) +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) + +# Class: (atom) + +AnnotationAssertion( "A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it."@en) +AnnotationAssertion( "This atom is closely related to ChEBI's atom, but not exactly equivalent to."@en) +AnnotationAssertion(rdfs:label "atom"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (molecule) + +AnnotationAssertion( "A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom."@en) +AnnotationAssertion( "This molecular entity is different than ChEBI's 'molecular entity'."@en) +AnnotationAssertion( "We would like to have cardinality restrictions on the logic, but there are some technical limitations."@en) +AnnotationAssertion(rdfs:label "molecule"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gross anatomical part) + +AnnotationAssertion( "A part of a multicellular organism that is a collection of cell components that are not all contained in one cell."@en) +AnnotationAssertion(rdfs:label "gross anatomical part"@en) +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome"@en) +AnnotationAssertion( "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'."@en) +AnnotationAssertion( "Includes virus - we will later have a class for cellular organisms."@en) +AnnotationAssertion(rdfs:label "organism"@en) +SubClassOf( ) + +# Class: (completely executed planned process) + +AnnotationAssertion(rdfs:label "completely executed planned process"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (complex of molecules) + +AnnotationAssertion( "A complex of two or more molecules that are not covalently bound."@en) +AnnotationAssertion(rdfs:label "complex of molecules"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (planned process) + +AnnotationAssertion( "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification."@en) +AnnotationAssertion(rdfs:label "planned process"@en) +SubClassOf( ) + +# Class: (characteristic) + +AnnotationAssertion(rdfs:label "characteristic"@en) + +# Class: (cellular_component) + +AnnotationAssertion( "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") +AnnotationAssertion(rdfs:label "cellular_component") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (protein-containing complex) + +AnnotationAssertion( "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.") +AnnotationAssertion( "This is not covalently bonded, which conflicts with changes to the parent definition."@en) +AnnotationAssertion(rdfs:label "protein-containing complex") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (virion component) + +AnnotationAssertion( "Any constituent part of a virion, a complete fully infectious extracellular virus particle.") +AnnotationAssertion(rdfs:label "virion component") +SubClassOf( ) + +# Class: (cellular anatomical entity) + +AnnotationAssertion( "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes."@en) +AnnotationAssertion( "Overlaps with some cellular components from GO"@en) +AnnotationAssertion(rdfs:label "cellular anatomical entity") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (data item) + +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "Pier: 'data, information or knowledge'. OR 'representation'"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) + +# Class: (directive information entity) + +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +SubClassOf( ) + +# Class: (plan) + +AnnotationAssertion( "A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process."@en) +AnnotationAssertion(rdfs:label "plan"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (data transformation) + +AnnotationAssertion( "A completely executed planned process that produces output data from input data."@en) +AnnotationAssertion(rdfs:label "data transformation"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (protein) + +AnnotationAssertion( "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.") +AnnotationAssertion(rdfs:label "protein") +SubClassOf( ) + +# Class: (amino acid chain) + +AnnotationAssertion( "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.") +AnnotationAssertion(rdfs:label "amino acid chain") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "Anatomical entity that has mass.") +AnnotationAssertion(rdfs:label "material anatomical entity") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (immaterial anatomical entity) + +AnnotationAssertion( "Anatomical entity that has no mass.") +AnnotationAssertion(rdfs:label "immaterial anatomical entity") +SubClassOf( ) +SubClassOf( ) + +# Class: (anatomical entity) + +AnnotationAssertion( "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.") +AnnotationAssertion(rdfs:label "anatomical entity") +EquivalentClasses( ObjectUnionOf( )) + + +) \ No newline at end of file diff --git a/src/ontology/imports/cob_terms.txt b/src/ontology/imports/cob_terms.txt new file mode 100644 index 0000000..e69de29 diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl index 9efb65c..8d946b9 100644 --- a/src/ontology/imports/external_import.owl +++ b/src/ontology/imports/external_import.owl @@ -10,12 +10,12 @@ Ontology( Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class(owl:Thing)) diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 372463c..4b96d88 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -15,9 +15,9 @@ Prefix(oboInOwl:=) Ontology( - + Annotation(dc:source ) -Annotation(owl:versionInfo "2025-07-02") +Annotation(owl:versionInfo "2026-01-31") Declaration(Class(obo:APOLLO_SV_00000008)) Declaration(Class(obo:APOLLO_SV_00000032)) diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index dc25c43..5d3b92e 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -7,14 +7,15 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2025-07-02") +Annotation(owl:versionInfo "2026-01-31") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -33,6 +34,7 @@ AnnotationAssertion( "Lindsay Cowell") AnnotationAssertion(rdfs:label "infectious disorder"@en) SubClassOf( ) +SubClassOf( ) # Class: (infection) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index c3a76db..cc9f2a1 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -7,14 +7,12 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2025-07-02") + +Annotation( ) +Annotation(owl:versionInfo "2026-02-10") -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) @@ -29,6 +27,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -40,12 +39,11 @@ Declaration(AnnotationProperty()) AnnotationAssertion( "is specified output of") AnnotationAssertion( ) -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion(rdfs:label "is specified output of"@en) SubObjectPropertyOf( ) -ObjectPropertyRange( ) # Object Property: (is member of organization) @@ -78,20 +76,20 @@ AnnotationAssertion(rdfs:label "has # Classes ############################ -# Class: (planned process) +# Class: (obsolete planned process) -AnnotationAssertion( "planned process") +AnnotationAssertion( "obsolete planned process") AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") AnnotationAssertion( ) AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") -AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process.") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.") AnnotationAssertion( "Bjoern Peters") AnnotationAssertion( "branch derived") +AnnotationAssertion( ) AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") -AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) -AnnotationAssertion(rdfs:label "planned process"@en) +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)") +AnnotationAssertion(rdfs:label "obsolete planned process") # Class: (disease stage) @@ -102,30 +100,12 @@ AnnotationAssertion( "PERSON: Bjoern peters") AnnotationAssertion(rdfs:label "disease stage"@en) -# Class: (organism) - -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "animal"@en) -AnnotationAssertion( "fungus"@en) -AnnotationAssertion( "plant"@en) -AnnotationAssertion( "virus"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") -AnnotationAssertion( "13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI.") -AnnotationAssertion( "GROUP: OBI Biomaterial Branch") -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) -AnnotationAssertion(rdfs:label "organism"@en) -SubClassOf( ) - # Class: (data transformation) AnnotationAssertion( "data transformation"@en) AnnotationAssertion( "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") AnnotationAssertion( ) -AnnotationAssertion( "A planned process that produces output data from input data."@en) +AnnotationAssertion( "A completely executed planned process that produces output data from input data."@en) AnnotationAssertion( "Elisabetta Manduchi"@en) AnnotationAssertion( "Helen Parkinson"@en) AnnotationAssertion( "James Malone"@en) @@ -138,7 +118,6 @@ AnnotationAssertion( "data processing"@en) AnnotationAssertion( "Branch editors"@en) AnnotationAssertion(rdfs:label "data transformation"@en) -SubClassOf( ) # Class: (dialysis) @@ -149,7 +128,6 @@ AnnotationAssertion( "PERSON:Kevin Clancy"@en) AnnotationAssertion( "OBI branch derived"@en) AnnotationAssertion(rdfs:label "dialysis"@en) -SubClassOf( ) ) \ No newline at end of file diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 2afbecc..85cee39 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -12,9 +12,9 @@ Prefix(oboInOwl:=) Ontology( - + Annotation(dc:source ) -Annotation(owl:versionInfo "2025-08-13") +Annotation(owl:versionInfo "2026-01-31") Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000030)) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index d48f9ff..808d1b8 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2025-07-02") + +Annotation( ) +Annotation(owl:versionInfo "2026-01-31") Declaration(Class()) Declaration(Class()) @@ -27,8 +27,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) @@ -111,6 +110,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -164,6 +165,44 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -173,6 +212,7 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -185,10 +225,11 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) @@ -329,6 +370,13 @@ AnnotationAssertion( "Add as annotation triples in the granting ontology"@en) AnnotationAssertion(rdfs:label "term replaced by"@en) +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:label "has_broad_synonym") + ############################ # Object Properties @@ -674,7 +722,7 @@ FunctionalObjectProperty() # Object Property: (before or simultaneous with) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion( "<="@en) AnnotationAssertion(rdfs:comment "Primitive instance level timing relation between events") AnnotationAssertion(rdfs:label "before or simultaneous with"@en) @@ -682,7 +730,7 @@ SubObjectPropertyOf( (before) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)"@en) AnnotationAssertion(rdfs:label "before"@en) SubObjectPropertyOf( ) @@ -690,7 +738,7 @@ TransitiveObjectProperty() # Object Property: (ends after) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) AnnotationAssertion(rdfs:label "ends after"@en) SubObjectPropertyOf( ) @@ -698,7 +746,7 @@ TransitiveObjectProperty() # Object Property: (immediately preceded by) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion( "starts_at_end_of") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) AnnotationAssertion(rdfs:label "immediately preceded by"@en) @@ -708,7 +756,6 @@ InverseObjectProperties( (immediately precedes) AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( "ends_at_start_of") AnnotationAssertion( "meets") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) @@ -827,7 +874,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "inverse of starts with") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "Allen") AnnotationAssertion(rdfs:label "starts"@en) SubObjectPropertyOf( ) @@ -840,7 +886,6 @@ AnnotationAssertion( ) AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "started by") AnnotationAssertion(rdfs:label "starts with"@en) SubObjectPropertyOf( ) @@ -852,7 +897,6 @@ TransitiveObjectProperty() AnnotationAssertion( ) AnnotationAssertion( "inverse of ends with") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion(rdfs:label "ends"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -863,7 +907,6 @@ InverseObjectProperties( ) AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "finished by") AnnotationAssertion(rdfs:label "ends with"@en) SubObjectPropertyOf( ) @@ -1144,6 +1187,28 @@ AnnotationAssertion(rdfs:label "imme SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (provides input for) + +AnnotationAssertion( "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.") +AnnotationAssertion( ) +AnnotationAssertion( "directly provides input for") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "provides input for"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (transitively provides input for) + +AnnotationAssertion( ) +AnnotationAssertion( "transitive form of directly_provides_input_for") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.") +AnnotationAssertion(rdfs:label "transitively provides input for"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (causally upstream of or within) AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") @@ -1567,6 +1632,7 @@ AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) # Object Property: (regulates characteristic) @@ -1699,7 +1765,6 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") SubClassOf( ) -DisjointClasses( ) # Class: (kinase activity) @@ -1723,39 +1788,11 @@ AnnotationAssertion( "curation status specification"@en) EquivalentClasses( ObjectOneOf( )) -# Class: (planned process) - -AnnotationAssertion( "planned process") -AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") -AnnotationAssertion( ) -AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") -AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process.") -AnnotationAssertion( "Bjoern Peters") -AnnotationAssertion( "branch derived") -AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") -AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) -AnnotationAssertion(rdfs:label "planned process"@en) -SubClassOf( ) - -# Class: (organism) - -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "animal"@en) -AnnotationAssertion( "fungus"@en) -AnnotationAssertion( "plant"@en) -AnnotationAssertion( "virus"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") -AnnotationAssertion( "13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI.") -AnnotationAssertion( "GROUP: OBI Biomaterial Branch") -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) -AnnotationAssertion(rdfs:label "organism"@en) -SubClassOf( ) +# Class: (disease) + +AnnotationAssertion( "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(rdfs:label "disease") +SubClassOf( ) # Class: (quality) @@ -1777,6 +1814,279 @@ SubClassOf( (Western Australian Mulga Shrublands Ecoregion) + +AnnotationAssertion( "Western Australia Ecoregion") +AnnotationAssertion( "WWF:AA1310") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1310") +AnnotationAssertion(rdfs:label "Western Australian Mulga Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Australasia Ecoregion) + +AnnotationAssertion( "https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands") +AnnotationAssertion(rdfs:label "Australasia Ecoregion"@en) + +# Individual: (Tirari-Sturt Stony Desert Ecoregion) + +AnnotationAssertion( "Southern central Australia Ecoregion"@en) +AnnotationAssertion( "WWF:AA1309") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1309") +AnnotationAssertion(rdfs:label "Tirari-Sturt Stony Desert Ecoregion") +ObjectPropertyAssertion( ) + +# Individual: (Simpson Desert Region) + +AnnotationAssertion( "Eastern central Australia Ecoregion") +AnnotationAssertion( "WWF:AA1308") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1308") +AnnotationAssertion(rdfs:label "Simpson Desert Region"@en) +ObjectPropertyAssertion( ) + +# Individual: (Pilbara Shrublands Ecoregion) + +AnnotationAssertion( "Western Australia Ecoregion") +AnnotationAssertion( "WWF:AA1307") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1307") +AnnotationAssertion(rdfs:label "Pilbara Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Carnarvon Xeric Shrublands Ecoregion) + +AnnotationAssertion( "Western coast of Australia Ecoregion") +AnnotationAssertion( "WWF:AA1301") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1301") +AnnotationAssertion(rdfs:label "Carnarvon Xeric Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Central Ranges Xeric Shrub Ecoregion) + +AnnotationAssertion( "Central Australia Ecoregion") +AnnotationAssertion( "WWF:AA1302") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1302") +AnnotationAssertion(rdfs:label "Central Ranges Xeric Shrub Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Gibson Desert Ecoregion) + +AnnotationAssertion( "Western central Australia") +AnnotationAssertion( "WWF:AA1303") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1303") +AnnotationAssertion(rdfs:label "Gibson Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (The Great Sandy-Tanami Desert Ecoregion) + +AnnotationAssertion( "Northwestern Australia") +AnnotationAssertion( "WWF:AA1304") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1304") +AnnotationAssertion(rdfs:label "The Great Sandy-Tanami Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Great Victoria Desert Ecoregion) + +AnnotationAssertion( "Southern Australia Ecoregion") +AnnotationAssertion( "WWF:AA1305") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1305") +AnnotationAssertion(rdfs:label "Great Victoria Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Nullarbor Plains Xeric Shrubland Ecoregion) + +AnnotationAssertion( "Southern Australia Ecoregion") +AnnotationAssertion( "WWF:AA1306") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1306") +AnnotationAssertion(rdfs:label "Nullarbor Plains Xeric Shrubland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Afrotropical Ecoregion) + +AnnotationAssertion( "https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands") +AnnotationAssertion(rdfs:label "Afrotropical Ecoregion"@en) + +# Individual: (Succulent Karoo Ecoregion) + +AnnotationAssertion( "Southern Africa: Southern Namibia into South Africa") +AnnotationAssertion( "WWF:AT1322") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1322") +AnnotationAssertion(rdfs:label "Succulent Karoo Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Yemen and Saudi Arabia Ecoregion) + +AnnotationAssertion( "WWF:AT1321") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1321") +AnnotationAssertion(rdfs:label "Yemen and Saudi Arabia Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Yemen, Saudi Arabia, and Oman Ecoregion) + +AnnotationAssertion( "WWF:AT1320") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1320") +AnnotationAssertion(rdfs:label "Yemen, Saudi Arabia, and Oman Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Somali Montane Xeric Woodland Ecoregion) + +AnnotationAssertion( "WWF:AT1319") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1319") +AnnotationAssertion(rdfs:label "Somali Montane Xeric Woodland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Socotran Archipelago Ecoregion) + +AnnotationAssertion( "Islands east of the Horn of Africa and south of Yemen Ecoregion") +AnnotationAssertion( "WWF:AT1318") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1318") +AnnotationAssertion(rdfs:label "Socotran Archipelago Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Red Sea Coastal Desert Ecoregion) + +AnnotationAssertion( "WWF:AT1317") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1317") +AnnotationAssertion(rdfs:label "Red Sea Coastal Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Namibian Savanna Woodland Ecoregion) + +AnnotationAssertion( "WWF:AT1316") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1316") +AnnotationAssertion(rdfs:label "Namibian Savanna Woodland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Namib Desert Ecoregion) + +AnnotationAssertion( "Africa: Namibia Ecoregion") +AnnotationAssertion( "WWF:AT1315") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1315") +AnnotationAssertion(rdfs:label "Namib Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Nama Karoo Ecoregion) + +AnnotationAssertion( "WWF:AT1314") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1314") +AnnotationAssertion(rdfs:label "Nama Karoo Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Masai Xeric Grasslands and Shrublands Ecoregion) + +AnnotationAssertion( "WWF:AT1313") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1313") +AnnotationAssertion(rdfs:label "Masai Xeric Grasslands and Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Madagascar Succulent Woodlands Ecoregion) + +AnnotationAssertion( "WWF:AT1312") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1312") +AnnotationAssertion(rdfs:label "Madagascar Succulent Woodlands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Madagascar Spiny Thickets Ecoregion) + +AnnotationAssertion( "WWF:AT1311") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1311") +AnnotationAssertion(rdfs:label "Madagascar Spiny Thickets Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Kaokoveld Desert Ecoregion) + +AnnotationAssertion( "WWF:AT1310") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1310") +AnnotationAssertion(rdfs:label "Kaokoveld Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Kalahari Xeric Savanna Ecoregion) + +AnnotationAssertion( "WWF:AT1309") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1309") +AnnotationAssertion(rdfs:label "Kalahari Xeric Savanna Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Ile Europa and Bassas da India Ecoregion) + +AnnotationAssertion( "WWF:AT1308") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1308") +AnnotationAssertion(rdfs:label "Ile Europa and Bassas da India Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Hobyo Grassland and Shrubland Ecoregion) + +AnnotationAssertion( "Eastern Africa: Somalia") +AnnotationAssertion( "WWF:AT1307") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1307") +AnnotationAssertion(rdfs:label "Hobyo Grassland and Shrubland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Oman and United Arab Emirates Ecoregion) + +AnnotationAssertion( "WWF:AT1306") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1306") +AnnotationAssertion(rdfs:label "Oman and United Arab Emirates Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Ethiopian Xeric Grasslands and Shrublands Ecoregion) + +AnnotationAssertion( "WWF:AT1305") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1305") +AnnotationAssertion(rdfs:label "Ethiopian Xeric Grasslands and Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Eritrean Coastal Desert Ecoregion) + +AnnotationAssertion( "WWF:AT1304") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1304") +AnnotationAssertion(rdfs:label "Eritrean Coastal Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (East Saharan Montane Xeric Woodland Ecoregion) + +AnnotationAssertion( "WWF:AT1303") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1303") +AnnotationAssertion(rdfs:label "East Saharan Montane Xeric Woodland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Oman, Yemen, and Saudi Arabia Ecoregion) + +AnnotationAssertion( "WWF:AT1302") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1302") +AnnotationAssertion(rdfs:label "Oman, Yemen, and Saudi Arabia Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Aldabra Island Xeric Scrub Ecoregion) + +AnnotationAssertion( "WWF:AT1301") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1301") +AnnotationAssertion(rdfs:label "Aldabra Island Xeric Scrub Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Indo-Malay Ecoregion) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Indo-Malay Ecoregion"@en) + +# Individual: (Thar Desert) + +AnnotationAssertion( ) +AnnotationAssertion( "WWF:IM1304") +AnnotationAssertion(rdfs:label "Thar Desert"@en) +ObjectPropertyAssertion( ) + +# Individual: (Northwestern Thorn Scrub Forests) + +AnnotationAssertion( ) +AnnotationAssertion( "WWF:IM1303") +AnnotationAssertion(rdfs:label "Northwestern Thorn Scrub Forests"@en) +ObjectPropertyAssertion( ) + +# Individual: (Solar radiation) + +AnnotationAssertion( "Stellar radiation emitted from Sol.") +AnnotationAssertion(rdfs:label "Solar radiation"@en) +ObjectPropertyAssertion( ) + # Individual: (example to be eventually removed) AnnotationAssertion( "example to be eventually removed"@en) @@ -1791,7 +2101,7 @@ AnnotationAssertion(rdfs:label "met # Individual: (organizational term) AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion( "The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release."@en) AnnotationAssertion(rdfs:label "organizational term"@en) # Individual: (ready for release) @@ -1874,6 +2184,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -1908,7 +2219,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) @@ -1919,17 +2230,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/mirror/obi.owl b/src/ontology/mirror/obi.owl index 3478afb..5f39d3b 100644 --- a/src/ontology/mirror/obi.owl +++ b/src/ontology/mirror/obi.owl @@ -7,15 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -82,7 +79,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2025-05-01 + 2025-12-18 @@ -104,29 +101,6 @@ - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - @@ -138,7 +112,6 @@ The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred label editor preferred term editor preferred term @@ -155,7 +128,6 @@ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage @@ -216,7 +188,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition definition textual definition @@ -232,7 +203,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note @@ -247,7 +217,6 @@ We also have the outstanding issue of how to aim different definitions to differ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor @@ -263,9 +232,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - alternative term @@ -279,7 +246,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source @@ -304,7 +270,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note @@ -360,7 +325,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from @@ -509,7 +473,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation @@ -522,7 +485,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language - has associated axiom(nl) @@ -535,7 +497,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) @@ -600,7 +561,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label @@ -912,12 +872,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1051,12 +1005,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1185,6 +1133,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -1194,12 +1148,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1295,12 +1243,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1316,12 +1258,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1414,18 +1336,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - has part @@ -1434,18 +1346,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + realized in @@ -1456,13 +1358,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1471,15 +1367,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + preceded by @@ -1488,50 +1379,43 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + precedes - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + executed by + + + + + + + + intended to realize - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + has plan + + + + + + + + intended plan process type @@ -1551,6 +1435,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is about A (currently) primitive relation that relates an information artifact to an entity. @@ -1654,11 +1539,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has specified input see is_input_of example_of_usage - The inverse property of is specified input of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters @@ -1690,11 +1575,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of @@ -1743,10 +1628,10 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - + has specified output - The inverse property of is specified output of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter @@ -1910,10 +1795,10 @@ instance level relation [GOC:cjm] - + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of @@ -2011,7 +1896,7 @@ level of radioactivity is_proxy_for level of toxicity - + achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' @@ -2130,7 +2015,7 @@ level of radioactivity is_proxy_for level of toxicity - + objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. @@ -2255,15 +2140,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + - @@ -2377,15 +2262,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2394,16 +2271,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - has characteristic @@ -2412,15 +2280,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -2429,16 +2289,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2447,11 +2298,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as @@ -2461,10 +2307,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes @@ -2474,15 +2316,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this catalysis function is a function of this enzyme + function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of @@ -2491,14 +2327,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this red color is a quality of this apple + quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of @@ -2507,14 +2338,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this investigator role is a role of this person + role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of @@ -2523,13 +2349,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + has function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function + has function @@ -2538,12 +2360,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this apple has quality this red color + has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality + has quality @@ -2552,13 +2371,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) + has role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role + has role @@ -2567,11 +2382,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - + has disposition a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition @@ -2580,8 +2393,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + inverse of has disposition + disposition of @@ -2590,47 +2404,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - derives from - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - + derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from derives from - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -2640,97 +2425,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in + located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by @@ -2739,11 +2446,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes @@ -2752,14 +2456,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - + has component - @@ -2767,11 +2467,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - has function realized in - capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of @@ -2779,9 +2480,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - surrounded by - x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by @@ -2796,15 +2496,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + inverse of surrounded by + surrounds + + + + - - - move to BFO? - Allen - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation + temporally related to + + temporally related to @@ -2812,61 +2518,50 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + starts inverse of starts with - Chris Mungall - Allen + starts - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + has output - + - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true + + inverse of enables + enabled by - + - - DEPRECATED bearer of - true + + + has member + has member is a mereological relation between a collection and an item. + + has member @@ -2888,6 +2583,41 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + has quantity + + + + + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + @@ -2972,518 +2702,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - @@ -3491,226 +2715,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - @@ -3718,183 +2733,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - @@ -3902,105 +2742,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - site - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -4008,439 +2751,40 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - material - MaterialEntity + material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - + immaterial entity - + - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - @@ -4449,7 +2793,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ insulin - A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the β cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. insulin @@ -4459,7 +2803,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -4471,7 +2815,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -4491,7 +2835,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + An organic heterobicyclic compound that consists of 2-oxohexahydro-1<em>H</em>-thieno[3,4-<em>d</em>]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin @@ -4501,9 +2845,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3β-hydroxy group. cholesterol @@ -4513,7 +2857,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -4525,7 +2869,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -4537,7 +2881,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -4549,9 +2893,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + A one-carbon compound with formula CO<small><sub>2</sub></small> in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide @@ -4563,7 +2907,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide @@ -4573,7 +2917,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -4585,7 +2929,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -4597,9 +2941,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + A member of the class of 2-benzofurans that is 2-benzofuran-1(3<em>H</em>)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2<i>E</i>)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by <em>Penicillium brevi-compactum, P. stoloniferum, P. echinulatum</em> and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. mycophenolic acid @@ -4609,7 +2953,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -4621,7 +2965,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -4645,9 +2989,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + progesterone - A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + A C<small><sub>21</sub></small>-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. progesterone @@ -4657,7 +3001,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogensulfite hydrogensulfite @@ -4668,7 +3012,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -4680,7 +3024,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -4692,9 +3036,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + testosterone - An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + An androstanoid having 17β-hydroxy and 3-oxo groups, together with unsaturation at C-4‒C-5.. testosterone @@ -4704,9 +3048,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + A hemoprotein that is the ferric (Fe<small><sup>3+</small></sup>) form of hemoglobin. methemoglobin @@ -4716,7 +3060,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -4728,9 +3072,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. + A 17α-hydroxy-C<small><sub>21</sub></small>-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -4740,7 +3084,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -4752,7 +3096,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -4764,7 +3108,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -4776,7 +3120,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -4788,7 +3132,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -4797,23 +3141,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - molecular entity - - - - - + cytochalasin cytochalasin @@ -4824,7 +3155,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -4836,21 +3167,35 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + A member of the class of <em>N</em>-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea + + + + + hormone + Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. + + hormone + + + + - + + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton @@ -4860,7 +3205,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + iron cation iron cation @@ -4871,7 +3216,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -4883,7 +3228,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -4895,7 +3240,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -4907,7 +3252,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -4919,7 +3264,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lead(0) lead(0) @@ -4930,9 +3275,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + A complex glycopeptide from <em>Streptomyces orientalis</em>. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria <em>Staphylococcus aureus</em> and <em>Clostridium difficile</em>. vancomycin @@ -4944,7 +3289,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + A racemate comprising equimolar amounts of (<i>R</i>)- and (<i>S</i>)-lactic acid. rac-lactic acid @@ -4954,7 +3299,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -4966,9 +3311,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + An androstanoid that is androst-5-ene substituted by a β-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. dehydroepiandrosterone @@ -4978,7 +3323,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -4989,7 +3334,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -5001,7 +3346,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -5013,7 +3358,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -5025,7 +3370,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydroxyl hydroxyl @@ -5036,20 +3381,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek δευτερον, second). deuterium atom + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -5061,7 +3415,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ruthenium atom ruthenium atom @@ -5090,7 +3444,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -5102,7 +3456,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5114,9 +3468,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red @@ -5126,7 +3480,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -5138,7 +3492,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methyl group An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. @@ -5147,14 +3501,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus @@ -5162,7 +3522,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + elemental oxygen elemental oxygen @@ -5173,7 +3533,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rare earth metal atom rare earth metal atom @@ -5184,7 +3544,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -5196,7 +3556,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium atom gadolinium atom @@ -5207,7 +3567,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + terbium atom terbium atom @@ -5220,7 +3580,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), <small>D</small>-ribose or 2-deoxy-<small>D</small>-ribose and phosphoric acid. nucleic acid @@ -5242,7 +3602,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amino acid A carboxylic acid containing one or more amino groups. @@ -5254,7 +3614,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer @@ -5267,7 +3627,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hemoglobin hemoglobin @@ -5278,7 +3638,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -5290,7 +3650,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium molecular entity gadolinium molecular entity @@ -5301,7 +3661,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -5310,10 +3670,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A particle smaller than an atom. + subatomic particle + + + + - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5325,9 +3696,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more <small>L</small>-glutamic acid units. folic acids @@ -5337,7 +3708,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium phosphate sodium phosphate @@ -5348,7 +3719,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5367,7 +3738,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5376,7 +3747,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin <small><sup>1</small></sup>/<small><sub>2</sub></small>. phosphorus-33 atom @@ -5456,7 +3827,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5467,7 +3838,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium ion calcium ion @@ -5478,7 +3849,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + magnesium cation Any magnesium ion that is positively charged. @@ -5510,7 +3881,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + A hydroxy steroid that consists of 5β-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3β-, 12β- and 14β-positions. It has been isolated from the plant species of the genus <em>Digitalis</em>. digoxigenin @@ -5520,7 +3891,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -5532,7 +3903,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + deoxyribonucleotide A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. @@ -5544,9 +3915,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + A cardenolide glycoside that is digitoxin β-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, <em>Digitalis lanata</em>, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. digoxin @@ -5567,7 +3938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -5579,7 +3950,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -5591,7 +3962,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -5603,15 +3974,26 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of γ rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 + + + + + resorufin + + resorufin + + + + @@ -5667,7 +4049,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -5679,7 +4061,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -5691,7 +4073,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -5703,7 +4085,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -5715,9 +4097,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two <em>N</em>-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5727,9 +4109,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent. N-methylisatoic anhydride @@ -5739,9 +4121,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (<i>S</i>)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5751,7 +4133,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -5763,9 +4145,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue @@ -5775,7 +4157,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -5787,7 +4169,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -5799,7 +4181,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -5811,7 +4193,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + thyroid stimulating hormone thyroid stimulating hormone @@ -5822,7 +4204,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Luteinizing hormone Luteinizing hormone @@ -5833,7 +4215,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Follicle stimulating hormone Follicle stimulating hormone @@ -5844,9 +4226,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + A hydroxycalciol that is vitamin D<small><sub>2</sub></small> in which the hydrogen at position 25 has been replaced by a hydroxy group. 25-hydroxyvitamin D2 @@ -5856,9 +4238,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + A primary amino compound that is <em>tert</em>-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7—9; p<em>K</em><small><sub>a</sub></small> = 8.3 at 20 °C; p<em>K</em><small><sub>a</sub></small> = 7.82 at 37 °C. tris @@ -5980,24 +4362,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + + cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. cell line cell - - - - - - - - - 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. - @@ -6109,10 +4487,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell @@ -6276,6 +4656,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte + A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. + + oligodendrocyte + + + + @@ -6437,11 +4829,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + experimentally modified cell in vitro @@ -6612,10 +5003,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mononuclear cell + mononuclear leukocyte A leukocyte with a single non-segmented nucleus in the mature form. - mononuclear cell + mononuclear leukocyte @@ -6692,14 +5083,297 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + - complex of molecules - A complex of two or more molecular entities that are not covalently bound. - - complex of molecules + + + + + + + A complex of two or more molecules that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A completely executed planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device @@ -6740,6 +5414,36 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental system process + + + + @@ -7014,7 +5718,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -7205,7 +5911,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RNA nuclease activity - Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + Catalysis of the cleavage of phosphodiester bonds in chains of RNA. RNA nuclease activity @@ -7227,6 +5933,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). @@ -7296,6 +6011,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of DNA repair + Any process that modulates the frequency, rate or extent of DNA repair. + + regulation of DNA repair + + + + @@ -7320,6 +6047,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + apoptotic process + A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. + + apoptotic process + + + + @@ -7344,6 +6083,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + plasma membrane organization + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + + plasma membrane organization + + + + @@ -7368,6 +6119,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryo implantation + Attachment of the blastocyst to the uterine lining. + + embryo implantation + + + + @@ -7396,10 +6159,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + + biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological process biological_process @@ -7549,6 +6318,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oxidoreductase activity + Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. + + oxidoreductase activity + + + + @@ -7585,6 +6366,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytolysis + The rupture of cell membranes and the loss of cytoplasm. + + cytolysis + + + + @@ -7669,6 +6462,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron differentiation + The process in which a relatively unspecialized cell acquires specialized features of a neuron. + + neuron differentiation + + + + + + + + + neuron projection development + The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). + + neuron projection development + + + + @@ -8190,7 +7007,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + @@ -8200,6 +7018,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. protein complex protein-containing complex @@ -8375,6 +7194,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hormone biosynthetic process + The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone biosynthetic process + + + + + + + + + hormone catabolic process + The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone catabolic process + + + + @@ -8439,6 +7282,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron projection + A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. + + neuron projection + + + + @@ -8475,6 +7330,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + @@ -8511,6 +7376,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + DNA-templated DNA replication maintenance of fidelity + A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair. + + DNA-templated DNA replication maintenance of fidelity + + + + @@ -8523,6 +7400,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synapse + The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. + + synapse + + + + @@ -8535,6 +7424,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte differentiation + The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. + + oligodendrocyte differentiation + + + + + + + + + anatomical structure development + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. + + anatomical structure development + + + + @@ -8607,6 +7520,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryonic process involved in female pregnancy + A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. + + embryonic process involved in female pregnancy + + + + + + + + + estrous cycle phase + The progression of physiological phases, occurring in the endometrium during the estrous cycle that recur at regular intervals during the reproductive years. The estrous cycle is an ovulation cycle where the endometrium is resorbed if pregnancy does not occur. + + estrous cycle phase + + + + @@ -8835,6 +7772,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of synapse maturation + Any process that modulates the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state. + + regulation of synapse maturation + + + + @@ -8967,6 +7916,37 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + neuron projection arborization + The process in which the anatomical structures of a neuron projection are generated and organized into branches. A neuron projection is any process extending from a neural cell, such as axons or dendrites. + + neuron projection arborization + + + + @@ -8991,6 +7971,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + mitotic DNA replication maintenance of fidelity + Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication. + + mitotic DNA replication maintenance of fidelity + + + + @@ -9015,6 +8007,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Severity + The intensity or degree of a manifestation. + + Severity + + + + @@ -9063,6 +8067,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + @@ -9116,9 +8130,10 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. + Pier: 'data, information or knowledge'. OR 'representation' information content entity @@ -9625,7 +8640,7 @@ clustering algorithm. - + documenting A planned process in which a document is created or added to by including the specified input in it. @@ -9650,7 +8665,7 @@ points together with a line. - + assigning a centrally registered identifier A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity @@ -10021,6 +9036,17 @@ No imports + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + @@ -10415,7 +9441,7 @@ No imports - + Viruses Viruses @@ -10560,10 +9586,19 @@ No imports + + + + + cellular organism + + + + - + Treponema pallidum Treponema pallidum @@ -10585,7 +9620,7 @@ No imports - + Bacteria eubacteria @@ -10597,7 +9632,7 @@ No imports - + Archaea Archaea @@ -10644,7 +9679,7 @@ No imports - + Eukaryota eucaryotes eukaryotes @@ -10753,6 +9788,17 @@ No imports + + + + + Pseudomonadati + + Pseudomonadati + + + + @@ -10982,7 +10028,7 @@ No imports - + Orientia tsutsugamushi Orientia tsutsugamushi @@ -11060,7 +10106,7 @@ No imports - + biological attribute biological attribute @@ -11223,30 +10269,21 @@ No imports - - - - - - - - - - - - - planned process + + obsolete planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + obsolete planned process + true @@ -11529,7 +10566,7 @@ objectives is a planned process. - + drug role @@ -11549,7 +10586,7 @@ objectives is a planned process. - + @@ -11584,7 +10621,7 @@ objectives is a planned process. - + physical document a book is a physical document @@ -11615,24 +10652,16 @@ objectives is a planned process. - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + obsolete processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + PERSON: Alan Ruttenberg + + + obsolete processed material + true @@ -11919,7 +10948,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -11934,7 +10963,7 @@ objectives is a planned process. - + @@ -12041,7 +11070,21 @@ objectives is a planned process. - + + + + + + + + + + + + + + + @@ -12127,7 +11170,7 @@ objectives is a planned process. - + @@ -12190,7 +11233,7 @@ objectives is a planned process. - + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 @@ -12332,38 +11375,21 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - - - - - - - - - - - - - - - - - material processing + + obsolete material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters + PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + OBI branch derived + + + obsolete material processing + true @@ -12478,7 +11504,7 @@ editor = PRS - + @@ -12867,7 +11893,7 @@ specimen can later be subject. - + @@ -13602,7 +12628,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13690,7 +12716,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13986,7 +13012,7 @@ for now. - + @@ -14028,10 +13054,16 @@ for now. + + + + + + plan The plan of researcher X to perform an experiment according to a protocol. - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived @@ -14193,8 +13225,8 @@ for now. - - + + @@ -14273,7 +13305,7 @@ for now. - + @@ -14372,14 +13404,14 @@ for now. - + - + @@ -14442,7 +13474,7 @@ need to add mobile phase as role - + @@ -14515,7 +13547,6 @@ need to add mobile phase as role - @@ -14629,7 +13660,7 @@ Proposal is to obsolete. - + @@ -14791,7 +13822,7 @@ Proposal is to obsolete. - + @@ -15143,7 +14174,7 @@ Proposal is to obsolete. - + @@ -15207,7 +14238,7 @@ Proposal is to obsolete. - + @@ -15468,7 +14499,7 @@ Proposal is to obsolete. - + @@ -15687,7 +14718,7 @@ activity) - + @@ -15708,7 +14739,7 @@ activity) - + @@ -16081,7 +15112,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16243,7 +15274,6 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra @@ -16258,7 +15288,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16327,7 +15357,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16627,7 +15657,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16737,7 +15767,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16747,7 +15777,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + manufacturing @@ -16950,7 +15980,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16963,7 +15993,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. @@ -17152,7 +16182,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -17366,7 +16396,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -17382,7 +16412,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -17689,7 +16719,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -17841,7 +16871,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18201,7 +17231,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18433,7 +17463,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -18802,13 +17832,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -19699,15 +18729,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - @@ -19775,26 +18796,55 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -20229,7 +19279,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20272,11 +19322,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + device setting @@ -20375,7 +19425,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20383,7 +19433,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20850,7 +19900,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + whole organism preparation @@ -21278,7 +20328,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21288,13 +20338,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + animal feeding @@ -21454,7 +20504,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21469,7 +20519,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21741,14 +20791,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -21811,7 +20861,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21879,7 +20929,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21905,7 +20955,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22057,7 +21107,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22081,7 +21131,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22211,7 +21261,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. @@ -22306,7 +21356,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + host role @@ -22526,7 +21576,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. @@ -22580,7 +21630,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22605,7 +21655,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs @@ -22630,13 +21680,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - - - + cloning vector @@ -22783,7 +21831,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site @@ -23255,6 +22302,7 @@ the role 'adjuvant role' inheres in some 'material entity' a + @@ -23489,11 +22537,11 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23565,7 +22613,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23598,7 +22646,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23689,14 +22737,14 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23765,7 +22813,6 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA Amplied DNA created by PCR @@ -23780,7 +22827,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23813,24 +22860,15 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule + true @@ -23884,7 +22922,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution @@ -23921,7 +22959,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -23935,7 +22973,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24193,7 +23231,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24214,7 +23252,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + pill A dose of medicine or placebo in the form of a small pellet. @@ -24273,7 +23311,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24281,7 +23319,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + measurement device A ruler, a microarray scanner, a Geiger counter. @@ -24406,7 +23444,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. @@ -24418,6 +23456,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -24446,7 +23485,7 @@ placeholder - + @@ -24474,7 +23513,7 @@ placeholder - + @@ -24495,7 +23534,7 @@ placeholder - + @@ -24577,23 +23616,14 @@ placeholder - - - - - - - - - - - - - primary structure of RNA molecule + + obsolete primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters - primary structure of RNA molecule + + obsolete primary structure of RNA molecule + true @@ -25144,7 +24174,7 @@ placeholder - + @@ -25467,7 +24497,7 @@ Person: Chris Stoeckert - + @@ -25478,7 +24508,7 @@ Person: Chris Stoeckert - + @@ -25884,7 +24914,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26031,7 +25061,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26055,7 +25085,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - + @@ -26773,8 +25803,8 @@ Updated both textual and logical definition. Both input and output material of f - + labeled specimen A specimen that has been modified in order to be able to detect it in future experiments @@ -26794,7 +25824,7 @@ Updated both textual and logical definition. Both input and output material of f - + infectious agent is a material entity bearing the disposition to infect an organism @@ -26903,7 +25933,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26955,7 +25985,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26963,7 +25993,7 @@ Updated both textual and logical definition. Both input and output material of f - + material separation device flow cytometer @@ -27045,7 +26075,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27122,7 +26152,7 @@ Updated both textual and logical definition. Both input and output material of f - + training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility @@ -27225,7 +26255,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27238,7 +26268,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27351,7 +26381,7 @@ Biochimie. 2010 Feb 18. - + service provider role @@ -27521,14 +26551,14 @@ Biochimie. 2010 Feb 18. - + - + processed specimen @@ -27593,7 +26623,7 @@ Biochimie. 2010 Feb 18. - + @@ -27813,7 +26843,7 @@ Biochimie. 2010 Feb 18. - + @@ -27844,7 +26874,7 @@ Biochimie. 2010 Feb 18. - + @@ -27852,7 +26882,7 @@ Biochimie. 2010 Feb 18. - + container A device that can be used to restrict the location of material entities over time @@ -27866,50 +26896,21 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - device + + obsolete device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - device + + + obsolete device + true @@ -27989,11 +26990,11 @@ In the examples above, a reagent is an operational component of a device, but th - + - + @@ -28004,7 +27005,7 @@ In the examples above, a reagent is an operational component of a device, but th sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data @@ -28111,7 +27112,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28531,7 +27532,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28853,7 +27854,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -28945,7 +27946,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -29332,7 +28333,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -29349,7 +28350,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30083,7 +29084,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30091,7 +29092,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) @@ -30109,7 +29110,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30117,7 +29118,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + perturbation device A homogenizer is a perturbation device. @@ -30137,7 +29138,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30153,7 +29154,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + environmental control device A growth chamber is an environmental control device. @@ -30446,7 +29447,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30532,7 +29533,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30629,7 +29630,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30731,7 +29732,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30751,7 +29752,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30797,7 +29798,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30823,7 +29824,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30883,7 +29884,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31032,7 +30033,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31052,7 +30053,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31283,7 +30284,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31355,7 +30356,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31457,7 +30458,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31477,7 +30478,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31651,7 +30652,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31719,7 +30720,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31864,7 +30865,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31918,7 +30919,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31978,7 +30979,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32046,7 +31047,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32066,7 +31067,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32126,7 +31127,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32365,7 +31366,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32418,7 +31419,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + individual organism identifier @@ -32577,7 +31578,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32676,7 +31677,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. @@ -32819,7 +31820,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -32830,7 +31831,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -33150,7 +32151,7 @@ All subtype will be defined by textual definition now. - + @@ -33166,11 +32167,11 @@ All subtype will be defined by textual definition now. - + - + service @@ -33320,15 +32321,6 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - @@ -33468,13 +32460,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -33486,7 +32478,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms @@ -37726,7 +36718,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -38335,7 +37327,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -40990,32 +39982,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - + genetic characteristics information @@ -43395,7 +42362,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -43424,7 +42391,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44305,7 +43272,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44361,7 +43328,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46020,10 +44987,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + @@ -46044,30 +45011,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + @@ -46727,7 +45684,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + material processing service @@ -47182,7 +46139,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + DNA sequence data @@ -49290,7 +48247,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 @@ -57712,7 +56669,7 @@ is realized in a specimen collection process. - + @@ -58378,7 +57335,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59378,7 +58335,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59730,7 +58687,7 @@ PMID: 23587118. - + @@ -59816,11 +58773,11 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - + - + reagent @@ -60824,7 +59781,7 @@ The following are NOT conclusions based on data: data themselves; results from p - + cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. @@ -61926,7 +60883,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. @@ -62006,7 +60963,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -62142,7 +61099,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay @@ -62298,7 +61255,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -62520,7 +61477,7 @@ PMID: 23587118. - + freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. @@ -62683,7 +61640,7 @@ PMID: 23587118. - + @@ -62718,7 +61675,7 @@ PMID: 23587118. - + @@ -62966,7 +61923,7 @@ PMID: 23587118. - + @@ -63205,7 +62162,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63213,7 +62170,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63276,7 +62233,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63287,7 +62244,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64575,6 +63532,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -64689,6 +63670,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -65665,7 +64670,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -65695,7 +64700,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -67343,11 +66348,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + @@ -70590,7 +69595,7 @@ https://www.doi.org/ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -70705,7 +69710,7 @@ https://www.doi.org/ - + determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. @@ -71707,7 +70712,7 @@ https://www.doi.org/ - + delivery form for hormonal replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. @@ -72310,7 +71315,7 @@ https://www.doi.org/ - + @@ -72321,7 +71326,7 @@ https://www.doi.org/ - + @@ -72884,11 +71889,11 @@ https://www.doi.org/ - + - + @@ -72909,11 +71914,11 @@ https://www.doi.org/ - + - + @@ -73264,7 +72269,7 @@ https://www.doi.org/ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. @@ -76336,7 +75341,7 @@ https://www.doi.org/ - + @@ -76358,7 +75363,7 @@ https://www.doi.org/ - + machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. @@ -78593,7 +77598,7 @@ https://www.doi.org/ 1 - + @@ -78660,7 +77665,7 @@ https://www.doi.org/ - + @@ -78668,7 +77673,7 @@ https://www.doi.org/ - + @@ -78691,7 +77696,7 @@ https://www.doi.org/ - + @@ -78713,7 +77718,7 @@ https://www.doi.org/ - + @@ -81919,7 +80924,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -81927,7 +80932,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + molecular label @@ -82001,7 +81006,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. @@ -82125,7 +81130,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA @@ -82893,7 +81898,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -83079,7 +82084,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -83185,7 +82190,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -83333,7 +82338,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + specimen collection device A device used to collect a specimen. @@ -83402,7 +82407,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -83466,7 +82471,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -83838,7 +82843,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + arthropod trap A device designed to catch arthropods. @@ -83897,7 +82902,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -83957,7 +82962,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + dipper for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. @@ -85421,11 +84426,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -85591,7 +84596,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. @@ -85607,7 +84612,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. @@ -86312,8 +85317,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + @@ -86701,7 +85705,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -86709,7 +85713,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87016,7 +86020,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87037,7 +86041,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. @@ -87414,7 +86418,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + common name of organism @@ -87502,7 +86506,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87513,7 +86517,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -88421,7 +87425,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -90922,7 +89926,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre leukapheresis - A blood harvesting process in which white blood cells are separated from a blood specimen. + A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis @@ -92822,7 +91826,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. @@ -93723,7 +92727,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -93731,7 +92735,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -94652,7 +93656,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf @@ -96267,7 +95271,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -97825,7 +96829,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -98314,7 +97318,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100728,7 +99732,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100736,7 +99740,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100759,7 +99763,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100850,7 +99854,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100858,7 +99862,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100881,7 +99885,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100972,7 +99976,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100980,7 +99984,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -101003,7 +100007,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -102928,14 +101932,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -102948,7 +101952,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasting @@ -102988,7 +101992,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasted @@ -103266,15 +102270,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - @@ -103357,7 +102352,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103791,7 +102785,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103833,7 +102827,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103874,7 +102868,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103942,7 +102936,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103966,7 +102960,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104022,7 +103016,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104033,7 +103027,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104080,7 +103074,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104091,7 +103085,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104138,7 +103132,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104149,7 +103143,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104196,7 +103190,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104207,7 +103201,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104254,7 +103248,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104265,7 +103259,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104312,7 +103306,2360 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + reproductive assay + + A physical examination of an organism that provides information about some reproductive process in that organism. + Jennifer Fostel + reproductive assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + vital sign assay + + An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). + Jennifer Fostel + vital sign assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood pressure assay + + A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. + Jennifer Fostel + blood pressure assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + heart rate variability assay + + A pulse rate assay that measures beat to beat variability in heart beats. + Jennifer Fostel + heart rate variability assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pulse rate assay + + A vital sign assay that measures the heart beat rate of an organism. + Jennifer Fostel + pulse rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + respiratory assay + + A vital sign assay that measures the quality of respiration / respiratory system of an organism + Jennifer Fostel + respiratory assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell differentiation assay + + A cytometry assay that monitors the differentiation stage of cells in culture. + Jennifer Fostel + cell differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell based DNA damage assay + + A cytometry assay that measures DNA damage in cells. + Jennifer Fostel + cell based DNA damage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell count assay + + A cytometry assay to determine the number of natural killer cells in a specimen + Jennifer Fostel + natural killer cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell percentage assay + + A cytometry assay that measures the percentage of natural killer cells in a specimen. + Jennifer Fostel + natural killer cell percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sperm count assay + + A cytometry assay to count the number of mature sperm in a specimen. + Jennifer Fostel + sperm count assay + + + + + + + + + survey administration assay + + An assay that obtains data from one or more participants by using a survey or questionnaire + Jennifer Fostel + survey administration assay + + + + + + + + + maximum data transformation + + A data transformation that has as its output the greatest value in the input data set. + Sebastian Duesing + maximum data transformation + + + + + + + + + minimum data transformation + + A data transformation that has as its output the least value in the input data set. + Sebastian Duesing + minimum data transformation + + + + + + + + + + + + + + + + + + + + + + + + + clinical history collection assay + A clinician asking a patient about the patient's smoking status. + + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. + Sebastian Duesing + HCC + clinical history collection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + disease severity assay + Measuring bone mineral density to determine the severity of osteoporosis. + + An assay that measures the severity of a disease in an organism. + Sebastian Duesing + HCC + disease severity assay + + + + + + + + + + + + + + + genetic characteristic assay + Determining a patient's HLA type. + + An assay that produces information about a genetic characteristic of an organism. + Sebastian Duesing + HCC + genetic characteristic assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood type assay + Identifying a person's ABO blood type. + + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. + Sebastian Duesing + https://medlineplus.gov/ency/article/003345.htm + blood type assay + + + + + + + + + manual muscle testing 8 score + + A clinical data item that quantifies the muscle function of a person based on the person's ability to hold a series of eight body positions that target different muscle groups. + Sebastian Duesing + MMT-8 + https://www.niehs.nih.gov/sites/default/files/research/resources/assets/docs/mmt8_grading_and_testing_procedures_for_the_abbreviated_8_muscle_groups_508.pdf + manual muscle testing 8 score + + + + + + + + + childhood myositis assessment scale score + + A clinical data item that quantifies the degree of muscle function in a child with myositis based on performance of 14 tasks associated with muscular strength and endurance. + Sebastian Duesing + CMAS + https://pubmed.ncbi.nlm.nih.gov/10524696/ + childhood myositis assessment scale score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary electrophoresis mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. + Sebastian Duesing + CE-MS + Thomas Payne + https://en.wikipedia.org/wiki/Capillary_electrophoresis–mass_spectrometry + https://github.com/obi-ontology/obi/issues/1904 + Thomas Payne + capillary electrophoresis mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite outgrowth assay + + A cell differentiation assay that detects neurite outgrowth and/or branching + The UBERON term for neurite is Neuron projection (GO:0043005; A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.). Multiplexed fluorescent imaging can be used to detect nuclei in neuronal cell bodies using Hoechst dye and neurites using anti-beta III-tubulin antibody staining. Commonly measured are neurite length, number and/or number of branch points (arborization). + Jennifer Fostel + neurite outgrowth assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuronal differentiation assay + + A cell differentiation assay that measures differentiation of neurons. + Jennifer Fostel + neuronal differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte differentiation assay + + A cell differentiation assay that measures differentiation of oligodendrocytes. + Jennifer Fostel + oligodendrocyte differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + regulation of synapse maturation assay + + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. + Synaptic puncta is this context is a small (0.5 to 2 um) distinct localized cluster of proteins involved in synaptic transmission. + Jennifer Fostel + regulation of synapse maturation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ames assay + + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. + The bacterial strains were originally constructed by Bruce Ames. Each carries a mutation in a gene involved in histidine synthesis. The cell requires histidine for growth but cannot produce it. The assay measures the creation of mutations that result in a return of function so that the cells can grow on a histidine-free medium. + Jennifer Fostel + Ames assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + micronucleus assay + + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. + The GO term "micronucleus" (GO:0031040) applies to protozoa but does not pertain to this case. Here micronucleus is a chromosome or fragment of a chromosome bounded by nuclear membrane that did not segregate properly at mitosis. + Jennifer Fostel + micronucleus assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PIG-a assay + + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. + The Pig-A gene encodes a product involved in biosynthesis of cell surface anchor glycosylphosphatidylinositol (GPI). + Jennifer Fostel + PIG-a assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin + + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. + Resazurin is the active ingredient in alamar blue; has a blue color and is non-fluorescent. Resorufin has pink color and is fluorescent. Detection of resorufin can be by absorbance or fluorescence. + Jennifer Fostel + Alamar Blue viability assay + cell viability assay based on detection of resorufin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using caspase abundance to detect apoptosis + + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis + Caspases 3 and 7 are frequently used as indicators of apoptosis. + Jennifer Fostel + cell death assay using caspase abundance to detect apoptosis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay + + A cell viability assay which measures the number or proportion of dead cells in a population. + Jennifer Fostel + cell death assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin + Resazurin (active ingredient in alamar blue and CellTiter blue reagents) has a blue color and is not fluorescent. Resorufin is pink and fluorescent. This assay uses the commercial reagent CellTiter Blue (Promega) containing resazurin and fluorescence to detect resorufin. + Jennifer Fostel + CellTiter Blue viability assay + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release + + A cell death assay that measures the release of intracellular LDH. + Jennifer Fostel + cell death assay detecting lactate dehydrogenase (LDH) release + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate + In this assay reagents are added so that LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate, and the NADH converts a tetrazolium salt to a colored formazan product in the presence of an electron acceptor. This formazan product is detected by absorbance quality. + Jennifer Fostel + Cytotox 96 assay + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ovulation assessment in rodent assay + + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. + Jennifer Fostel + Corpus luteum count + ovulation assessment in rodent assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + macroscopic examination of material anatomical entity assay + + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. + Jennifer Fostel + macroscopic examination of material anatomical entity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pathological macroscopic examination of specimen assay + + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. + one objective of this assay is to provide information about the character and extent of changes present and to inform on the cause of death. + Jennifer Fostel + Gross pathology assessment + pathological macroscopic examination of specimen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle assay based on tissue morphology + + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. + Jennifer Fostel + estrous cycle assay based on tissue morphology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo + + An organism development assay performed with a late embryo stage subject. + one objective of this assay is to assess anatomical structures and identify developmental phenotype + Jennifer Fostel + fetal examination + organism development assay in late embryo + + + + + + + + + + + + + + + + + + + + @@ -104323,7 +105670,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104341,24 +105688,26 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - reproductive assay + pregnancy assessment based on tissue morphology assay - A physical examination of an organism that provides information about some reproductive process in that organism. + A histological assay that measures the number of implantation sites in an organism. + An implantation site in this context is the site in the endometrium where the fertilized egg attaches and embeds itself to begin development Jennifer Fostel - reproductive assay + implantation site count + pregnancy assessment based on tissue morphology assay - + - - + + @@ -104370,7 +105719,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104381,7 +105730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104399,24 +105748,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - vital sign assay + cell death assay using vital dye - An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. + Living cells exclude Trypan blue Jennifer Fostel - vital sign assay + cell death assay using vital dye - + - - + + @@ -104428,7 +105778,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104439,7 +105789,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104451,30 +105801,44 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + - + - blood pressure assay + neurite length assay - A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. + A neurite is a neuronal process greater than 10 um extending from a neuron. Jennifer Fostel - blood pressure assay + neurite length assay - + - - + + @@ -104486,7 +105850,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104497,7 +105861,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104511,8 +105875,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + + + + + + + + @@ -104521,24 +105892,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - heart rate variability assay + neurite degree of arborization assay - A pulse rate assay that measures beat to beat variability in heart beats. + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes Jennifer Fostel - heart rate variability assay + neurite branch point count + neurite degree of arborization assay - + - - + + @@ -104550,7 +105922,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104561,7 +105933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104575,8 +105947,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + + + + + + + + @@ -104585,24 +105964,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - pulse rate assay + neurite count assay - A vital sign assay that measures the heart beat rate of an organism. + A cytometry assay that measures the number of neurites in a cultured specimen. + A neurite is a neuronal process greater than 10 um extending from a neuron. Jennifer Fostel - pulse rate assay + neurite count assay - + - - + + @@ -104614,7 +105994,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104625,7 +106005,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104639,34 +106019,30 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - + - - - - + + + + + + - respiratory assay + neuron count assay - A vital sign assay that measures the quality of respiration / respiratory system of an organism + A cytometry assay that measures the number of neurons in a sample Jennifer Fostel - respiratory assay + neuron count assay - + - - + + @@ -104678,7 +106054,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104689,7 +106065,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104701,30 +106077,68 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - cell differentiation assay + cell-body-associated presynaptic puncta count assay - A cytometry assay that monitors the differentiation stage of cells in culture. + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - cell differentiation assay + cell-body-associated presynaptic puncta count assay - + - - + + @@ -104736,7 +106150,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104747,7 +106161,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104767,10 +106181,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -104778,35 +106192,49 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + - + - cell based DNA damage assay + dendrite-associated presynaptic puncta count assay - A cytometry assay that measures DNA damage in cells. + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - cell based DNA damage assay + dendrite-associated presynaptic puncta count assay - + - - + + @@ -104818,7 +106246,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104829,7 +106257,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104841,30 +106269,44 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + - + - natural killer cell count assay + synapse per neuron assay - A cytometry assay to determine the number of natural killer cells in a specimen + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - natural killer cell count assay + synapse per neuron assay - + - - + + @@ -104876,7 +106318,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104887,7 +106329,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104905,24 +106347,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - natural killer cell percentage assay + absorbance quality detection assay - A cytometry assay that measures the percentage of natural killer cells in a specimen. + An assay that measures the absorbance quality of the evaluant + the unit of this assay is absorbance unit (UO:0000269) Jennifer Fostel - natural killer cell percentage assay + absorbance quality detection assay - + - - + + @@ -104931,10 +106374,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -104942,17 +106385,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + @@ -104963,29 +106396,110 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + - sperm count assay + hormone assay - A cytometry assay to count the number of mature sperm in a specimen. + The analyte assay that measures the abundance of a hormone in a specimen. Jennifer Fostel - sperm count assay + hormone assay - + - - - survey administration assay + + + electrocardiograph + + An instrument for recording the changes of electrical potential occurring during the heartbeat used especially in diagnosing abnormalities of heart action. + Jennifer Fostel + https://www.merriam-webster.com/dictionary/electrocardiograph + electrocardiograph + + + + + + + + + biotelemeter - An assay that obtains data from one or more participants by using a survey or questionnaire + A measurement device that also transmits the measurement information from a biological material to a distant station. Jennifer Fostel - survey administration assay + biotelemeter + + + + + + + + + multi-electrode array plate + + A measurement device consisting of grid of tightly spaced microscopic electrodes that can detect the electrical signals of cells in close proximity. + Multielectrode arrays can be embedded in the bottom of a well and cells can be cultured over the electrodes for passive, noninvasive monitoring of electrical activity. + Jennifer Fostel + multi-electrode array plate + + + + + + + + + Transepithelial Electrical Resistance (TEER) device + + A measurement device that measures monolayer barrier integrity via measurement of membrane potential and electrical resistance across a cell monolayer in culture. + Jennifer Fostel + Transepithelial Electrical Resistance (TEER) device + + + + + + + + + randomized clinical trial + + A clinical trial in which the participants are divided by chance into separate groups that compare different treatments or other interventions. Using chance to divide people into groups means that the groups will be similar and that the effects of the treatments they receive can be compared more fairly. At the time of the trial, it is not known which treatment is best. + Sebastian Duesing + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/randomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + randomized clinical trial + + + + + + + + + non-randomized clinical trial + + A clinical trial in which the participants are not assigned by chance to different treatment groups. Participants may choose which group they want to be in, or they may be assigned to the groups by the researchers. + Sebastian Duesing + nonrandomized clinical trial + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/nonrandomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + non-randomized clinical trial @@ -105032,7 +106546,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. @@ -105047,7 +106561,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + chimera An organism which contains cells or tissues with a different genotype @@ -105081,7 +106595,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -105155,31 +106668,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - organism - animal - fungus - plant - virus + + obsolete organism + animal + fungus + plant + virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + WEB: http://en.wikipedia.org/wiki/Organism + + + obsolete organism + true @@ -105340,7 +106844,7 @@ This issue is outside the scope of OBI. - + @@ -105350,7 +106854,7 @@ This issue is outside the scope of OBI. - + xenograft @@ -105369,7 +106873,7 @@ This issue is outside the scope of OBI. - + @@ -105484,7 +106988,7 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- - + screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] @@ -105514,7 +107018,6 @@ change biomaterial to material in definition - synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme @@ -105533,7 +107036,7 @@ DS: Is this synthetic an oxymoron to the biomaterial? - + @@ -105653,7 +107156,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + + + + + + + + + + + + + + + @@ -105685,7 +107202,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -107840,7 +109357,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - + @@ -109697,7 +111214,7 @@ determinations of compounds. - + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. @@ -109784,7 +111301,7 @@ determinations of compounds. - + @@ -109812,7 +111329,7 @@ determinations of compounds. - + @@ -110069,7 +111586,6 @@ determinations of compounds. - denatured polymer Is a polymer which has lost secondary or tertiary structure @@ -110094,7 +111610,7 @@ determinations of compounds. - + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 @@ -110188,7 +111704,6 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 @@ -110207,7 +111722,7 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - + @@ -110215,8 +111730,8 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 + - genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 @@ -110402,7 +111917,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110423,7 +111938,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110456,7 +111971,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110489,11 +112004,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + - + @@ -110538,7 +112053,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110687,7 +112202,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -110753,7 +112268,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110774,7 +112289,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110806,14 +112321,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + - + @@ -110876,7 +112391,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110904,7 +112419,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -110931,7 +112446,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. @@ -111017,7 +112532,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -111235,7 +112750,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112165,7 +113680,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112199,7 +113714,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + particle delivery vessel FC 500 particle delivery vessel @@ -112285,7 +113800,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112307,7 +113822,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112549,7 +114064,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112640,7 +114155,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112711,7 +114226,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112830,7 +114345,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113199,7 +114714,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113374,7 +114889,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113449,7 +114964,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -114107,7 +115622,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114136,14 +115651,14 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114159,7 +115674,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114213,7 +115728,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114230,13 +115745,13 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114316,7 +115831,7 @@ Relates to the creation of a class 'selection rule' - + exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. @@ -114436,7 +115951,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114463,11 +115978,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + @@ -114479,7 +115994,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114675,7 +116190,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114698,7 +116213,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114892,7 +116407,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114914,7 +116429,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114977,7 +116492,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115074,7 +116589,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115096,7 +116611,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115152,7 +116667,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115226,7 +116741,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115266,7 +116781,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115287,17 +116802,17 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + - + @@ -115383,7 +116898,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115779,7 +117294,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115874,7 +117389,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115995,7 +117510,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116110,8 +117625,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + - @@ -116139,7 +117654,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116167,7 +117682,7 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti - + @@ -116235,7 +117750,7 @@ addition of has_role restriction - + @@ -116266,7 +117781,7 @@ old defintion: A mixture (collection) of cell components created by rupturing of - + @@ -116320,7 +117835,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -116350,7 +117864,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. @@ -116675,7 +118189,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + Immunization in vivo @@ -116767,7 +118281,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116883,7 +118397,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116928,7 +118442,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116936,7 +118450,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. @@ -117204,7 +118718,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen @@ -118000,19 +119513,20 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - blood harvesting + blood specimen collection - A material separation where blood is taken from an organism. + A specimen collection in which blood is collected from an organism. IEDB + blood harvesting IEDB - blood harvesting + blood specimen collection @@ -118200,7 +119714,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen @@ -122002,7 +123515,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -147892,18 +149405,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - phenotype - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - - phenotype - - - - @@ -147960,7 +149461,7 @@ realizes some 'host of immune response role' - + treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process @@ -148044,7 +149545,7 @@ realizes some 'host of immune response role' - + parasite organism An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. @@ -148068,7 +149569,7 @@ realizes some 'host of immune response role' - + quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities @@ -148404,7 +149905,7 @@ realizes some 'host of immune response role' - + physical object quality A quality which inheres in a continuant. @@ -148413,6 +149914,30 @@ realizes some 'host of immune response role' + + + + + full-spectrum EM radiation quality + An EM radiation quality that is independent of the EM wavelength range. + + full-spectrum EM radiation quality + + + + + + + + + absorption quality + A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. + + absorption quality + + + + @@ -148918,6 +150443,16 @@ realizes some 'host of immune response role' + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + @@ -149026,12 +150561,40 @@ realizes some 'host of immune response role' + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + protein antithrombin III is a protein + An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein @@ -149279,6 +150842,16 @@ realizes some 'host of immune response role' + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + @@ -149484,6 +151057,18 @@ realizes some 'host of immune response role' + + + + + modified histone + A histone that contains one or more amino acid modifications. + + modified histone + + + + @@ -149519,7 +151104,7 @@ realizes some 'host of immune response role' - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule @@ -149807,6 +151392,18 @@ realizes some 'host of immune response role' + + + + + late embryo + An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. + + late embryo + + + + @@ -149846,7 +151443,18 @@ realizes some 'host of immune response role' + + + + + + + + + + + material anatomical entity Anatomical entity that has mass. @@ -149855,6 +151463,17 @@ realizes some 'host of immune response role' + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + @@ -150095,6 +151714,24 @@ realizes some 'host of immune response role' + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + @@ -150863,6 +152500,18 @@ realizes some 'host of immune response role' + + + + + corpus luteum + A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. + + corpus luteum + + + + @@ -151319,6 +152968,18 @@ realizes some 'host of immune response role' + + + + + phenotype + A phenotypic effect related to http://www.w3.org/2002/07/owl#Thing. + + phenotype + + + + @@ -151336,7 +152997,7 @@ realizes some 'host of immune response role' vaccination - A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. + Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response. vaccination @@ -155642,25 +157303,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - geographic location A reference to a place on the Earth, by its name or by its geographical location. @@ -155678,48 +157320,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -155742,195 +157342,6 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/mirror/ro.owl b/src/ontology/mirror/ro.owl index a3d3910..fff2d40 100644 --- a/src/ontology/mirror/ro.owl +++ b/src/ontology/mirror/ro.owl @@ -9,7 +9,6 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" - xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -17,15 +16,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2025-03-05 + 2025-12-17 https://github.com/oborel/obo-relations/ @@ -42,12 +40,6 @@ - - - - - - @@ -289,17 +281,6 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - @@ -1196,54 +1177,18 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1286,12 +1231,6 @@ Where we have an annotation assertion - - - - - - @@ -1322,30 +1261,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1366,12 +1281,6 @@ Where we have an annotation assertion - - - - - - @@ -1476,30 +1385,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1682,7 +1567,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by @@ -1788,6 +1672,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y + lacks_part + + + + + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) + lacks_plasma_membrane_part + + + + @@ -2356,9 +2258,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure. http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by + innervated by @@ -2736,7 +2643,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + <= Primitive instance level timing relation between events @@ -2753,7 +2660,6 @@ Examples include: the relationship between two channels collected simultaneously x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with @@ -2766,7 +2672,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before @@ -2779,7 +2685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends @@ -2810,7 +2716,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -2827,7 +2733,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by @@ -2840,7 +2746,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts @@ -2857,7 +2763,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts before @@ -2873,7 +2779,6 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland ends_at_start_of meets @@ -2890,7 +2795,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) @@ -2905,7 +2810,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + d during @@ -2923,7 +2828,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + o overlaps @@ -3580,13 +3485,29 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + - + + + + + + + + + + + + + + + + + @@ -3609,6 +3530,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + @@ -3617,6 +3542,18 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. @@ -4271,7 +4208,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of starts with - Chris Mungall Allen starts @@ -4289,7 +4225,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall started by starts with @@ -4361,7 +4296,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ends with - Chris Mungall ends @@ -4377,7 +4311,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall finished by ends with @@ -5017,7 +4950,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -6247,8 +6180,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. @@ -6821,6 +6754,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A relation that holds between a disease or an organism and a phenotype @@ -8257,8 +8191,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -8531,8 +8465,10 @@ the a supports either the existence of b, or the truth value of b. + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI + indicates is marker for @@ -8870,6 +8806,67 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + x is an ectomycorrhizal host of y if and only if x is a plant (Plantae) whose roots form an intercellular interface (aka Hartig net) with fungus (Fungi) y. This interface consists of highly branched hyphae forming a latticework between epidermal and cortical root cells. + + + + An ectomycorrhiza is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. The mycobiont is often from the phyla Basidiomycota and Ascomycota, and more rarely from the Zygomycota. Ectomycorrhizae form on the roots of around 2% of plant species, usually woody plants, including species from the birch, dipterocarp, myrtle, beech, willow, pine and rose families. Research on ectomycorrhizae is increasingly important in areas such as ecosystem management and restoration, forestry, and agriculture. Unlike other mycorrhizal relationships, such as arbuscular mycorrhiza and ericoid mycorrhiza, ectomycorrhizal fungi do not penetrate their host's cell wall. Instead they form an entirely intercellular interfaces known as the Hartig net, consisting of highly branched hyphae forming a latticework between epidermal and cortical root cells. + ectomycorrhizal host of + + + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + inverse of ectomycorrhizal host of + + has ectomycorrhizal host + + + + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + x is an arbuscular mycorrhizal host of y if and only if x is a vascular plant (Plantae) whose cortical cells of the roots are penetrated by fungus (Fungi) y and form arbuscules. + + + + An arbuscular mycorrhiza (AM) (plural mycorrhizae) is a type of mycorrhiza in which the symbiont fungus (Arbuscular mycorrhizal fungi, or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza (not to be confused with ectomycorrhiza). They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered. Arbuscular mycorrhizae are formed by fungi in the subphylum Glomeromycotina and some fungi from the Mucoromycotina. These subphyla, along with the Mortierellomycotina, form the phylum Mucoromycota, a sister clade of the more well-known and diverse dikaryan fungi. AM fungi help plants to capture nutrients such as phosphorus, sulfur, nitrogen and micronutrients from the soil. It is believed that the development of the arbuscular mycorrhizal symbiosis played a crucial role in the initial colonisation of land by plants and in the evolution of the vascular plants. It has been said that it is quicker to list the plants that do not form endomycorrhizae than those that do. This symbiosis is a highly evolved mutualistic relationship found between fungi and plants, the most prevalent plant symbiosis known, and AMF is found in 80% of vascular plant families in existence today. + arbuscular mycorrhizal host of + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + inverse of arbuscular mycorrhizal host of + + + has arbuscular mycorrhizal host + + + + @@ -9762,8 +9759,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9775,8 +9772,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9808,7 +9805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. @@ -9899,7 +9896,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -10855,6 +10852,24 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + The information in a blueprint specifies the dimensions of a building. + The information in a recipe specifies what interredients to use and the steps needed to prepare a meal. + The information in a software program specifies the order of computations. + A relation between information and an entity such that the information serves as a rule or guide if the entity is an occurrent, or the information serves as a model if the entity is a continuant. + + 2025-06-16T17:08:04Z + prescribes + specifies + information specifies + https://www.ontologyrepository.com/CommonCoreOntologies/prescribes + + + + @@ -10910,6 +10925,17 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + inverse of 'has symptom' + + 2025-06-16T17:42:05Z + symptom of + + + + @@ -10942,6 +10968,29 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + Inverse of information specifies. + + 2025-06-16T17:13:17Z + specified by information + + + + + + + + + Inverse relation of 'is marker for'. + + 2025-07-14T20:57:25Z + has marker + + + + @@ -11316,6 +11365,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context. + Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals. + + + has substitutable entity + + + + @@ -11437,86 +11499,321 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - This relation groups relations between diseases and any other kind of entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - - 2018-09-26T00:00:32Z - disease relationship + + + A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + provides clinical information for - + - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - - 2018-09-26T01:08:58Z - results in changes to anatomical or cellular structure + + + A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue. + An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype. + https://orcid.org/0000-0001-5809-9523 + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + diagnostic for - + - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - TODO: Add homeomorphy axiom - - - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - + + + Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression. + A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The status of 'd' refers to disease progression/remission or treatment response. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors status of - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - + - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - + + + The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates response to - - - - Similarity that results from common evolutionary origin. - - + + + + + + + + The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug. + +Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + predicts effect of + + + + + + + + + A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + prognostic for + + + + + + + + + As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + assesses toxicity of + + + + + + + + + The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates risk of developing + + + + + + + + + An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy. + A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates clinical effect of + + + + + + + + + The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors effect of + + + + + + + + + The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers: + - 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest; + - 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent; + - 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent. + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors exposure to + + + + + + + + + A polyubiquitin has_constituent_monomer some ubiquitin. + An amino acid chain has_constituent_monomer at least two amino acid residues. + A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer 'm' if and only if P has_component multiple instances of 'm' and each instance of 'm' is covalently attached to another instance of 'm'. + + Usage note: The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows the number of instances of 'm' to be indicated. + has constituent monomer + + + + + + + + + + Charged tRNA (i.e., aminoacyl-tRNA) is a tRNA that is covalently_bound_to some amino acid. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of covalent interactions. + + Such entities will colocalize at all times of the interaction. + covalently bound to + + + + + + + + + + Holo-calmodulin is a calmodulin that is non-covalently_bound_to calcium. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions. + + Such entities will colocalize at all times of the interaction. + non-covalently bound to + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + @@ -11529,7 +11826,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - + homoplasous to analogy @@ -11553,7 +11850,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - + ECO:0000075 homocracous to @@ -11579,7 +11876,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - + analogy Convergence usually implies a notion of adaptation. @@ -11602,7 +11899,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. @@ -11625,7 +11922,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - + ECO:0000071 MI:2163 @@ -11652,7 +11949,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - + homology ECO:0000080 @@ -11687,7 +11984,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - + ECO:0000067 biological homologous to @@ -11713,7 +12010,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - + atavism rudiment @@ -11737,7 +12034,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - + MeSH:Synteny SO:0000860 @@ -11764,7 +12061,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - + SO:0000854 SO:0000859 @@ -11792,7 +12089,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - + syntenic paralogous to duplicon @@ -11817,7 +12114,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - + syntenic orthologous to in syntenic orthology relationship with @@ -11839,7 +12136,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - + fractional homology partial homologous to @@ -11868,7 +12165,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - + MeSH:Structural_Homology,_Protein protein structural homologous to @@ -11892,7 +12189,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - + pseudogene SO:non_functional_homolog_of @@ -11916,7 +12213,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - + ECO:00000060 SO:0000855 @@ -11946,7 +12243,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). @@ -11970,7 +12267,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - + 1 to 1 homologous to 1:1 homology @@ -11995,7 +12292,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - + 1 to 1 orthologous to 1:1 orthology @@ -12020,7 +12317,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - + ohnologous to homoeology @@ -12044,7 +12341,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - + in-paralogous to inparalogy @@ -12068,7 +12365,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - + alloparalogy out-paralogous to @@ -12092,7 +12389,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - + pro-orthologous to in pro-orthology relationship with @@ -12115,7 +12412,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - + semi-orthologous to The converse of pro-orthologous. @@ -12139,7 +12436,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - + serial homologous to homonomy @@ -12162,7 +12459,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - + heterochronous homologous to heterochrony @@ -12186,7 +12483,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - + juvenification pedomorphosis @@ -12210,7 +12507,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - + in peramorphosis relationship with @@ -12231,7 +12528,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - + in progenesis relationship with @@ -12253,7 +12550,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - + juvenilization neotenous to @@ -12277,7 +12574,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - + mimicrous to in mimicry relationship with @@ -12300,7 +12597,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - + 1 to many orthologous to 1:many orthology @@ -12327,7 +12624,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - + many to many homologous to many-to-many homology @@ -12351,7 +12648,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - + 1 to many homologous to one-to-many homology @@ -12376,7 +12673,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - + apomorphous to synapomorphy @@ -12399,7 +12696,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - + plesiomorphous to symplesiomorphy @@ -12424,7 +12721,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - + deep genetic homology deep homologous to @@ -12451,7 +12748,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - + hemiplasous to in hemiplasy relationship with @@ -12473,7 +12770,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - + gametologous to in gametology relationship with @@ -12495,7 +12792,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - + MeSH:Chromosome_Pairing chromosomal homologous to @@ -12519,7 +12816,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - + many to many orthologous to many-to-many orthology @@ -12548,7 +12845,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - + within-species paralogous to in within-species paralogy relationship with @@ -12570,7 +12867,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - + between-species paralogous to The genes have diverged before a speciation event. @@ -12593,7 +12890,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - + post-displacement in postdisplacement relationship with @@ -12615,7 +12912,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - + in hypermorphosis relationship with @@ -12637,7 +12934,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - + synologous to in synology relationship with @@ -12661,7 +12958,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - + ECO:0000080 isoorthologous to @@ -12684,7 +12981,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - + tandem paralogous to iterative paralogy @@ -12710,7 +13007,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - + apomorphic tendency cryptic homology @@ -12742,7 +13039,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - + generative homology syngenous to @@ -12768,7 +13065,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - + 1:1 paralogy apparent 1:1 orthology @@ -12795,7 +13092,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. @@ -12819,7 +13116,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - + equivalogous to This may include examples of orthology, paralogy and xenology. @@ -12842,7 +13139,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - + interologous to in interology relationship with @@ -12865,7 +13162,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - + functional similarity in functional equivalence relationship with @@ -12888,7 +13185,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - + iterative homologous to in iterative homology relationship with @@ -12910,7 +13207,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - + duplicate xenology multiple xenology @@ -12934,7 +13231,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - + plerologous to This phenomenon is usually due to gene conversion process. @@ -12958,7 +13255,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. @@ -12983,7 +13280,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - + heterotopy in homeosis relationship with @@ -13007,7 +13304,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. @@ -13031,7 +13328,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - + axis paramorphism in paramorphism relationship with @@ -13054,7 +13351,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - + regulogous to in regulogy relationship with @@ -13446,6 +13743,38 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + completely executed planned process + + + + @@ -13462,6 +13791,16 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A processed material entity which is designed to be capable of a process. + device + + + + @@ -13487,14 +13826,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu An environmental system which can sustain and allow the growth of an ecological population. - - EcoLexicon:habitat LTER:238 SWEETRealm:Habitat - A habitat's specificity to an ecological population differentiates it from other environment classes. See Buttigieg et al. (2016; https://doi.org/10.1186/s13326-016-0097-6) for an explanation of ENVO's treatement of habitats. 3,849 of such habitat classes are available here: https://github.com/EnvironmentOntology/envo-habitats + https://en.wikipedia.org/wiki/Habitat + A habitat's specificity to an ecological population differentiates it from other environment classes. habitat + + + + An environmental system which can sustain and allow the growth of an ecological population. + EnvO:EnvO + @@ -13600,7 +13944,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3781009 Reactome:R-HSA-3788724 Reactome:R-HSA-3797226 - Reactome:R-HSA-400267 Reactome:R-HSA-4332236 Reactome:R-HSA-446877 Reactome:R-HSA-450358 @@ -13649,6 +13992,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-975118 Reactome:R-HSA-975147 Reactome:R-HSA-9758604 + Reactome:R-HSA-9766227 Reactome:R-HSA-9793444 Reactome:R-HSA-9793485 Reactome:R-HSA-9793679 @@ -13665,6 +14009,10 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9834070 Reactome:R-HSA-9861563 Reactome:R-HSA-9861640 + Reactome:R-HSA-9929350 + Reactome:R-HSA-9934753 + Reactome:R-HSA-9948301 + Reactome:R-HSA-9954721 ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity @@ -14083,12 +14431,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3797226 Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) - - - - Reactome:R-HSA-400267 - BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins - @@ -14249,7 +14591,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-69598 - Ubiquitination of phosphorylated Cdc25A + Ubiquitination of phosphorylated CDC25A @@ -14377,6 +14719,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9758604 Ubiquitination of IKBKG by TRAF6 + + + + Reactome:R-HSA-9766227 + MDM2 mediates CDH1 ubiquitination + @@ -14473,6 +14821,30 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9861640 CTLH E3 ligase ubiquitinates PKM-1 + + + + Reactome:R-HSA-9929350 + Ubiquitination of CD274 by BTRC-SCF E3-ligase complex + + + + + Reactome:R-HSA-9934753 + CBLL1 ubiquitinates CDH1 + + + + + Reactome:R-HSA-9948301 + ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit + + + + + Reactome:R-HSA-9954721 + NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide + @@ -14509,7 +14881,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z @@ -14638,44 +15009,22 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process - + - + - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - + - + assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. @@ -14694,7 +15043,6 @@ objectives is a planned process. - container A device that can be used to restrict the location of material entities over time @@ -14705,56 +15053,6 @@ objectives is a planned process. - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - @@ -14950,6 +15248,7 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 + FAO:0000001 FMA:305751 FMA:67135 GAID:781 @@ -14967,6 +15266,7 @@ This issue is outside the scope of OBI. connected biological structure UBERON:0000061 + @@ -15335,73 +15635,596 @@ This issue is outside the scope of OBI. - + - - example to be eventually removed - example to be eventually removed + + + + 2019-03-05T17:25:21Z + Western Australia Ecoregion + WWF:AA1310 + https://www.worldwildlife.org/ecoregions/aa1310 + Western Australian Mulga Shrublands Ecoregion - + - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete + + + 2019-03-05T17:51:32Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Australasia Ecoregion - + - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term + + + + 2019-03-05T17:52:41Z + Southern central Australia Ecoregion + WWF:AA1309 + https://www.worldwildlife.org/ecoregions/aa1309 + Tirari-Sturt Stony Desert Ecoregion - + - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release + + + + 2019-03-05T17:54:35Z + Eastern central Australia Ecoregion + WWF:AA1308 + https://www.worldwildlife.org/ecoregions/aa1308 + Simpson Desert Region - + - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete + + + + 2019-03-05T17:56:13Z + Western Australia Ecoregion + WWF:AA1307 + https://www.worldwildlife.org/ecoregions/aa1307 + Pilbara Shrublands Ecoregion - + - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated + + + + 2019-03-05T18:10:52Z + Western coast of Australia Ecoregion + WWF:AA1301 + https://www.worldwildlife.org/ecoregions/aa1301 + Carnarvon Xeric Shrublands Ecoregion - + - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + + + + 2019-03-05T18:12:28Z + Central Australia Ecoregion + WWF:AA1302 + https://www.worldwildlife.org/ecoregions/aa1302 + Central Ranges Xeric Shrub Ecoregion + + + + + + + + + + 2019-03-05T18:15:11Z + Western central Australia + WWF:AA1303 + https://www.worldwildlife.org/ecoregions/aa1303 + Gibson Desert Ecoregion + + + + + + + + + + 2019-03-05T18:17:15Z + Northwestern Australia + WWF:AA1304 + https://www.worldwildlife.org/ecoregions/aa1304 + The Great Sandy-Tanami Desert Ecoregion + + + + + + + + + + 2019-03-05T18:24:06Z + Southern Australia Ecoregion + WWF:AA1305 + https://www.worldwildlife.org/ecoregions/aa1305 + Great Victoria Desert Ecoregion + + + + + + + + + + 2019-03-05T18:26:16Z + Southern Australia Ecoregion + WWF:AA1306 + https://www.worldwildlife.org/ecoregions/aa1306 + Nullarbor Plains Xeric Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:01:41Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Afrotropical Ecoregion + + + + + + + + + + 2019-03-06T22:02:37Z + Southern Africa: Southern Namibia into South Africa + WWF:AT1322 + https://www.worldwildlife.org/ecoregions/at1322 + Succulent Karoo Ecoregion + + + + + + + + + + 2019-03-06T22:07:38Z + WWF:AT1321 + https://www.worldwildlife.org/ecoregions/at1321 + Arabian Peninsula: Yemen and Saudi Arabia + Yemen and Saudi Arabia Ecoregion + + + + + + + + + + 2019-03-06T22:11:38Z + WWF:AT1320 + https://www.worldwildlife.org/ecoregions/at1320 + Arabian Peninsula: Yemen, Saudi Arabia, and Oman + Yemen, Saudi Arabia, and Oman Ecoregion + + + + + + + + + + 2019-03-06T22:13:00Z + WWF:AT1319 + https://www.worldwildlife.org/ecoregions/at1319 + Somali montane xeric woodlands ecoregion + Somali Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-06T22:15:07Z + Islands east of the Horn of Africa and south of Yemen Ecoregion + WWF:AT1318 + https://www.worldwildlife.org/ecoregions/at1318 + Socotran Archipelago Ecoregion + + + + + + + + + 2019-03-06T22:18:55Z + WWF:AT1317 + https://www.worldwildlife.org/ecoregions/at1317 + Red Sea Coastal Desert Ecoregion + + + + + + + + + 2019-03-06T22:20:56Z + WWF:AT1316 + https://www.worldwildlife.org/ecoregions/at1316 + Namibian Savanna Woodland Ecoregion + + + + + + + + + 2019-03-06T22:24:28Z + Africa: Namibia Ecoregion + WWF:AT1315 + https://www.worldwildlife.org/ecoregions/at1315 + Namib Desert Ecoregion + + + + + + + + + 2019-03-06T22:26:15Z + WWF:AT1314 + https://www.worldwildlife.org/ecoregions/at1314 + Nama Karoo Ecoregion + + + + + + + + + 2019-03-06T22:28:43Z + WWF:AT1313 + https://www.worldwildlife.org/ecoregions/at1313 + Masai Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-06T22:30:23Z + WWF:AT1312 + https://www.worldwildlife.org/ecoregions/at1312 + Madagascar Succulent Woodlands Ecoregion + + + + + + + + + 2019-03-06T22:31:29Z + WWF:AT1311 + https://www.worldwildlife.org/ecoregions/at1311 + Madagascar spiny desert ecoregion + Madagascar Spiny Thickets Ecoregion + + + + + + + + + 2019-03-06T22:39:32Z + WWF:AT1310 + https://www.worldwildlife.org/ecoregions/at1310 + Africa: Coastal Namibia and Angola Ecoregion + Kaokoveld Desert Ecoregion + + + + + + + + + 2019-03-06T22:42:47Z + WWF:AT1309 + https://www.worldwildlife.org/ecoregions/at1309 + Kalahari Xeric Savanna Ecoregion + + + + + + + + + 2019-03-06T22:44:54Z + WWF:AT1308 + https://www.worldwildlife.org/ecoregions/at1308 + Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion + Ile Europa and Bassas da India Ecoregion + + + + + + + + + 2019-03-06T22:46:58Z + Eastern Africa: Somalia + WWF:AT1307 + https://www.worldwildlife.org/ecoregions/at1307 + Hobyo Grassland and Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:54:57Z + WWF:AT1306 + https://www.worldwildlife.org/ecoregions/at1306 + Arabian Peninsula: Oman and United Arab Emirates Ecoregion + Oman and United Arab Emirates Ecoregion + + + + + + + + + 2019-03-07T00:08:06Z + WWF:AT1305 + https://www.worldwildlife.org/ecoregions/at1305 + Ethiopian Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-07T00:11:29Z + WWF:AT1304 + https://www.worldwildlife.org/ecoregions/at1304 + Eritrean Coastal Desert Ecoregion + + + + + + + + + 2019-03-07T00:13:33Z + WWF:AT1303 + https://www.worldwildlife.org/ecoregions/at1303 + North central Africa: Eastern Chad and small area of western Sudan + East Saharan Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-07T00:16:12Z + WWF:AT1302 + https://www.worldwildlife.org/ecoregions/at1302 + Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion + Oman, Yemen, and Saudi Arabia Ecoregion + + + + + + + + + 2019-03-07T00:18:09Z + WWF:AT1301 + https://www.worldwildlife.org/ecoregions/at1301 + Aldabra Island Xeric Scrub Ecoregion + + + + + + + + 2019-04-26T23:38:50Z + + Indo-Malay Ecoregion + + + + + + + + + 2019-04-26T23:40:13Z + + WWF:IM1304 + Southern Asia: Western India into Pakistan + Thar Desert + + + + + + + + + 2019-04-27T00:12:51Z + + WWF:IM1303 + Southern Asia: Eastern India and western Pakistan + Northwestern Thorn Scrub Forests + + + + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + envoAtmo + envoPolar + Arctic front + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + + + + + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + envoAtmo + envoPolar + Antarctic front + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + + + + + + + + + + Stellar radiation emitted from Sol. + Solar radiation + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -15493,6 +16316,69 @@ binary, and takes no temporal argument. + + + + researcher + Nicole Vasilevsky + + + + + researcher + + + + + + Nicole Vasilevsky + + + + + + + + + researcher + Darren A. Natale + + + + + researcher + + + + + + Darren A. Natale + + + + + + + + + researcher ORCID ID = 0000-0001-5948-3092 + Marta Costa + + + + + researcher ORCID ID = 0000-0001-5948-3092 + + + + + + Marta Costa + + + + + @@ -15535,6 +16421,27 @@ binary, and takes no temporal argument. + + + + researcher + Katja S Schulz + + + + + researcher + + + + + + Katja S Schulz + + + + + @@ -15556,6 +16463,27 @@ binary, and takes no temporal argument. + + + + researcher + David P Hill + + + + + researcher + + + + + + David P Hill + + + + + @@ -15598,6 +16526,48 @@ binary, and takes no temporal argument. + + + + American epidemiologist and ontologist + Melissa Haendel + + + + + American epidemiologist and ontologist + + + + + + Melissa Haendel + + + + + + + + + researcher + Jennifer Deegan + + + + + researcher + + + + + + Jennifer Deegan + + + + + @@ -15619,6 +16589,48 @@ binary, and takes no temporal argument. + + + + researcher + Alexander D Diehl + + + + + researcher + + + + + + Alexander D Diehl + + + + + + + + + researcher + Matthew Brush + + + + + researcher + + + + + + Matthew Brush + + + + + @@ -15682,6 +16694,48 @@ binary, and takes no temporal argument. + + + + researcher + Tanya Z Berardini + + + + + researcher + + + + + + Tanya Z Berardini + + + + + + + + + researcher + Sabrina Toro + + + + + researcher + + + + + + Sabrina Toro + + + + + @@ -15703,6 +16757,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0002-5260-9315 + Patrick Ray + + + + + Researcher ORCID=0000-0002-5260-9315 + + + + + + Patrick Ray + + + + + @@ -15955,6 +17030,27 @@ binary, and takes no temporal argument. + + + + researcher + Terrence F Meehan + + + + + researcher + + + + + + Terrence F Meehan + + + + + @@ -16015,6 +17111,33 @@ binary, and takes no temporal argument. Charles Tapley Hoyt + + + + + + + researcher + Vasundra Touré + + + + + researcher + + + + + + Vasundra Touré + + + + + + + + @@ -16045,7 +17168,8 @@ binary, and takes no temporal argument. failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg failed exploratory term @@ -16073,21 +17197,26 @@ binary, and takes no temporal argument. placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. placeholder removed terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. term imported term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. term split @@ -16216,6 +17345,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Add as annotation triples in the granting ontology is allocated id range + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. @@ -16378,7 +17513,7 @@ No imports The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. out of scope @@ -16394,66 +17529,84 @@ No imports domain entity does not exist + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + 2025-06-02 + preferred label for community + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms + 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms + 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms + 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms + 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms + 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants + 2023-03-03 UK spelling synonym A synonym type for common misspellings + 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. + 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name + 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + 2023-09-30 INN International Nonproprietary Name @@ -16461,18 +17614,21 @@ No imports nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. + 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + 2023-11-01 acronym A serial number such as "12324X"; a stop sign; a written proper name such as "OBI An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 2024-03-25 has symbol @@ -16597,15 +17753,15 @@ No imports - - - + + + @@ -16616,6 +17772,7 @@ No imports + if effector directly negatively regulates X, its parent MF directly negatively regulates X @@ -16623,9 +17780,9 @@ No imports - - - + + + @@ -16634,9 +17791,9 @@ No imports - - - + + + @@ -16650,9 +17807,9 @@ No imports - - - + + + @@ -16660,6 +17817,7 @@ No imports + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16667,9 +17825,9 @@ No imports - - - + + + @@ -16678,9 +17836,9 @@ No imports - - - + + + @@ -16693,17 +17851,29 @@ No imports - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16711,9 +17881,9 @@ No imports - - - + + + @@ -16721,24 +17891,13 @@ No imports - - - + + + + - - - - - - - - - - - - - + @@ -16748,13 +17907,24 @@ No imports - - - - + + + - + + + + + + + + + + + + + @@ -16766,9 +17936,9 @@ No imports - - - + + + @@ -16776,9 +17946,10 @@ No imports - - - + + + + @@ -16792,9 +17963,9 @@ No imports - - - + + + @@ -16809,9 +17980,9 @@ No imports - - - + + + @@ -16819,9 +17990,10 @@ No imports - - - + + + + @@ -16835,9 +18007,9 @@ No imports - - - + + + @@ -16852,9 +18024,9 @@ No imports - - - + + + @@ -16862,9 +18034,10 @@ No imports - - - + + + + @@ -16878,9 +18051,9 @@ No imports - - - + + + @@ -16895,9 +18068,9 @@ No imports - - - + + + @@ -16905,9 +18078,10 @@ No imports - - - + + + + @@ -16921,9 +18095,9 @@ No imports - - - + + + @@ -16931,9 +18105,6 @@ No imports - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg @@ -16941,9 +18112,9 @@ No imports - - - + + + @@ -16952,36 +18123,12 @@ No imports - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -16992,9 +18139,9 @@ No imports - - - + + + @@ -17002,18 +18149,16 @@ No imports - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -17022,25 +18167,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -17051,9 +18183,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17061,9 +18193,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP @@ -17071,8 +18200,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17081,9 +18210,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17091,10 +18220,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -17110,9 +18238,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17127,9 +18255,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17138,37 +18266,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -17179,9 +18281,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17189,8 +18291,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction @@ -17198,9 +18298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17208,26 +18308,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17238,9 +18324,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17248,7 +18334,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg reg edge from input to regulatory subfunction @@ -17256,9 +18341,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17266,26 +18351,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17296,9 +18367,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17306,7 +18377,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct positive reg edge from input to regulatory subfunction @@ -17314,9 +18384,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17324,26 +18394,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17354,9 +18410,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17364,7 +18420,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - effector input is compound function input + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg @@ -17372,9 +18430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17383,12 +18441,36 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17400,8 +18482,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17409,17 +18491,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - Input of effector is input of its parent MF + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts - - - - + + + @@ -17428,12 +18511,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17444,9 +18540,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17454,17 +18550,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly regulates X, its parent MF directly regulates X + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP - - - - + + + @@ -17473,12 +18570,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17487,11 +18597,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - + + + + + @@ -17499,7 +18609,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17507,9 +18616,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17517,13 +18626,38 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17534,9 +18668,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17544,7 +18678,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly negatively regulates X, its parent MF directly negatively regulates X + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction @@ -17552,9 +18687,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17563,12 +18698,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17579,9 +18727,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17589,7 +18737,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct neg reg edge from input to regulatory subfunction @@ -17597,9 +18745,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17608,12 +18756,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17623,29 +18784,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct positive reg edge from input to regulatory subfunction @@ -17653,9 +18803,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17664,12 +18814,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17679,28 +18842,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + + effector input is compound function input @@ -17708,9 +18861,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17719,9 +18872,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17735,9 +18888,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17745,6 +18898,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + Input of effector is input of its parent MF @@ -17752,9 +18906,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17763,9 +18917,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17779,9 +18933,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17789,6 +18943,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly regulates X, its parent MF directly regulates X @@ -17796,9 +18951,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17807,9 +18962,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17823,9 +18978,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17833,6 +18988,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17840,9 +18996,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17851,9 +19007,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17867,9 +19023,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/src/ontology/ogms-base.owl b/src/ontology/ogms-base.owl index 0c6c8a4..f97f932 100644 --- a/src/ontology/ogms-base.owl +++ b/src/ontology/ogms-base.owl @@ -1,20 +1,49 @@ + xmlns:terms="http://purl.org/dc/terms/" + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - None - - The Ontology for General Medical Science - 2025-07-02 + + Matthew Diller + Alan Ruttenberg + Albert Goldfain + Anand Kumar + Barry Smith + Bill Hogan + Brian Aevermann + Cornelius Rosse + Daniel Merico + Jie Zheng + Lindsay Cowell + Richard Scheuermann + Sivaram Arabandi + Werner Ceusters + 2009-08-07 + The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. + +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + Ontology for General Medical Science + + http://creativecommons.org/licenses/by/4.0/ + The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + +The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl + +The OGMS developer site is https://github.com/OGMS/ogms + +If you are interested in participating in the development of OGMS, please send email to matthew.diller@nih.gov + 2026-01-31 @@ -30,15 +59,81 @@ - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + @@ -48,9 +143,9 @@ - + - + @@ -65,10 +160,1526 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T10:18:02Z + clinical finding + + + + + + + + + A series of statements representing health-relevant qualities of a patient and of a patient's family. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T10:18:59Z + clinical history + + + + + + + + + A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T10:20:20Z + clinical picture + + + + + + + + + An interpretation of an image that is the output of a clinical evaluation and supports an inference to an assertion about some quality of a patient. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T10:21:10Z + clinical finding from image + + + + + + + + + A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T10:21:58Z + laboratory finding + + + + + + + + + A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T10:22:44Z + preclinical finding + + + + + + + + + A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant. + note: defined class + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06 + symptom + + + + + + + + + A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:12:33Z + manifestation of a disease + + + + + + + + + A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T11:13:49Z + phenotype + + + + + + + + The class sign has been replaced by three seperate classes which reflect the different types of signs possible. + obsolete_sign + true + + + + + + + + + A manifestation of a disease that is detectable in a clinical history taking or physical examination. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:15:43Z + clinical manifestation of a disease + + + + + + + + + A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:16:50Z + preclinical manifestation of a disease + + + + + + + + + A clinically abnormal phenotype. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:18:05Z + clinical phenotype + + + + + + + + + A clinically abnormal phenotype that is characteristic of a single disease. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:18:39Z + disease phenotype + + + + + + + + + A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:19:17Z + vital sign + + + + + + + + + A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:20:25Z + predisposition to disease of type X + + + + + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:21:20Z + disease + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:22:01Z + homeostasis + + + + + + + + + A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:23:07Z + genetic predisposition to disease of type X + + + + + + + + + A disease whose physical basis is an acquired genetic disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:24:05Z + acquired genetic disease + + + + + + + + + A disease whose physical basis is a constitutional genetic disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:24:59Z + constitutional genetic disease + + + + + + + + + Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:26:44Z + altered homeostasis + + + + + + + + + Homeostasis of a type that is not clinically abnormal. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:27:28Z + normal homeostasis + + + + + + + + + A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:36:24Z + configuration + + + + + + + + + A configuration which deviates in some way from a canonical configuration for a particular organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:36:58Z + pathological physical configuration + + + + + + + + + A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:39:44Z + disorder + + + + + + + + + A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:40:27Z + epigenetic disorder + + + + + + + + + A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:41:14Z + genetic disorder + + + + + + + + + A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:43:09Z + acquired genetic disorder + + + + + + + + + A genetic disorder inherited during conception that is part of all cells in the organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:43:44Z + constitutional genetic disorder + + + + + + + + + A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:49:16Z + clinical history taking + + + + + + + + + A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:49:49Z + clinical laboratory test + + + + + + + + + A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T11:50:18Z + physical examination + + + + + + + + + A process in an organism that leads to a subsequent disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:53:07Z + etiological process + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:53:49Z + bodily process + + + + + + + + + A bodily process that is clinically abnormal. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:54:29Z + pathological bodily process + + + + + + + + + The totality of all processes through which a given disease instance is realized. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:55:44Z + disease course + + + + + + + + + A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:56:26Z + +10212020 + +for definition use: +http://purl.obolibrary.org/obo/PATO_0001863 + chronic disease course + + + + + + + + + A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:57:09Z + progressive disease course + + + + + + + + + A disease course that terminates in a return to normal homeostasis. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:57:44Z + transient disease course + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:58:22Z + _undefined primitive term + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:59:24Z + clinically abnormal + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T12:00:09Z + physical basis + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T12:00:39Z + realization + + + + + + + + + The representation of a conclusion of a diagnostic process. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T12:42:23Z + diagnosis + + + + + + + + + A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-26T10:31:34Z + normal value + + + + + + + + + TODO: Define, relate to disorder, and place in the OGMS hierarchy. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:14:59Z + pathological formation + + + + + + + + + An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:14:05Z + pathological anatomical structure + + + + + + + + + TODO: Define, relate to disorder, and place in the OGMS hierarchy. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:15:17Z + portion of pathological body substance + + + + + + + + + A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:17:07Z + pathological transformation + + + + + + + + + A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:17:24Z + pathological derivation + + + + + + + + + TODO: Define. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:17:47Z + pathological invasion + + + + + + + + + TODO: Define. + Albert Goldfain + creation date: 2009-11-24T04:51:11Z + physical examination finding + + + + + + + + + An aggregate of organisms of the same type. + Albert Goldfain + creation date: 2009-11-24T04:51:11Z + organism population + + + + + + + + + A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage. + Albert Goldfain + https://philarchive.org/rec/SMITAO-12 + creation date: 2009-11-24T04:51:11Z + pain + + + + + + + + + A pattern of signs and symptoms that typically co-occur. + Albert Goldfain + creation date: 2009-11-24T04:51:11Z + syndrome + + + + + + + + + An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. + Albert Goldfain + creation date: 2010-01-25T04:51:11Z + extended organism + + + + + + + + + A communication from a patient about something they perceive as being abnormal about their body or life. + Albert Goldfain + creation date: 2010-01-25T04:51:11Z + patient symptom report + + + + + + + + + A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism. + Albert Goldfain + congenital malformation + creation date: 2010-03-31T04:51:11Z + congenital disorder + + + + + + + + + A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process + Albert Goldfain + creation date: 2010-03-31T04:51:11Z + treatment + + + + + + + + + A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course. + Albert Goldfain + creation date: 2010-03-31T04:51:11Z + convalescence + + + + + + + + + A process which has as parts all the processes in which a given organism is participant. + Albert Goldfain +Richard Scheuermann +Sagar Jain + creation date: 2010-03-31T04:51:11Z + +EDIT: 10 NOV 2015 + life course + + + + + + + + + A hypothesis about some future part of a disease course. + Albert Goldfain + creation date: 2010-03-31T12:42:23Z + prognosis + + + + + + + + + A disease course with an acute onset + Albert Goldfain + creation date: 2010-07-19T11:57:44Z + +10212020 + +for definition use + +http://purl.obolibrary.org/obo/PATO_0000389 + acute disease course + + + + + + + + + A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling. + Albert Goldfain +Richard Scheuermann +Sagar Jain + creation date: 2010-07-19T11:57:44Z + +Updated: 10 NOV 2015 + inflammatory process + + + + + + + + + A planned process with the objective to improve or maintain the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient + Albert Goldfain +Sagar Jain + creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18 + health care process + + + + + + + + + A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter + Albert Goldfain + creation date: 2011-02-21T09:57:44Z + health care encounter + + + + + + + + + A health care process in which a person is admitted to a hospital for treatment, diagnosis, or monitoring. + Albert Goldfain + creation date: 2011-02-21T09:57:44Z + hospitalization + + + + + + + + + TODO + Albert Goldfain + creation date: 2011-02-21T09:57:44Z + outpatient encounter + + + + + + + + + A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night. + Albert Goldfain + creation date: 2011-02-21T09:57:44Z + inpatient encounter + + + + + + + + + A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention. + Albert Goldfain + creation date: 2011-02-21T09:57:44Z + emergency department encounter + + + + + + + + + A disorder that involves some structural damage that is immediately caused by a catastrophic external force. + At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level. + Albert Goldfain +Sagar Jain + creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015 + injury + + + + + + + + + A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder. + Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question. + Albert Goldfain + creation date: 2011-09-20T09:57:44Z + disease prophylaxis + + + + + + + + + A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output). + Albert Goldfain + creation date: 2011-09-20T09:57:44Z + diagnostic process + + + + + + + + + A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease. + A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course. + Albert Goldfain +Richard Scheuermann +Sagar Jain + recurrent + 10 NOV 2015 + relapse + + + + + + + + + A disease stage which is characterized by the lack of a manifestation of a disease + A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased. + Albert Goldfain +Richard Scheuermann +Sagar Jain + 10 NOV 2015 + remission + + + + + + + + + A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient. + 2017-04-18 + Sagar Jain + ancillary health care process + + + + + + + + + A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + creation: 16MAY2017 + Sagar Jain + health care process assay + + + + + + + + + A health care process which results in physical changes in a specified input material + creation: 16MAY2017 + Sagar Jain + health care process biomaterial transformation + + + + + + + + + A health care process that produces output from input data + creation: 16MAY2017 + Sagar Jain + health care process data transformation + + + + + + + + + A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process. + Creation date: 2018-11-27 + prophylactic treatment + + + + + + + + + A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process. + Creation data: 2018-11-27 + therapeutic procedure + + + + + + + + + A therapeutic procedure that uses synthetic or naturally-occurring chemicals + creation date: 2018-11-27 + chemotherapy procedure + + + + + + + + + A therapeutic procedure that uses immune system derived entities. + creation date: 2018-11-27 + immunotherapy procedure + + + + + + + + + A therapeutic procedure that uses physical conditioning + creation date: 2018-11-27 + physical therapy procedure + + + + + + + + + A therapeutic procedure that uses radiation. + creation date: 2018-11-27 + radiation therapy procedure + + + + + + + + + A disease stage characterized by the lack of symptoms associated with a given disease + creation date: 2018-11-27 + asymptomatic + + + + + + + + + A disease stage that marks the beginning of a disease + creation date 2018-11-27 + onset + + + + + + + + + A disease stage with a rapid unfolding of signs and symptoms + creation date 2018-11-27 + acute onset + + + + + + + + + A remission which is characterized by a prolonged lack of all manifestations of a disease + complete remission + + + + + + + + + A remission which is characterized by a prolonged lack of some manifestations of a disease + partial remission + + + + + + + + + A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist + creation date: 2018-11-27 + recovered from disease + + + + + + + + + A data item that is about a patient and is the specified output of a health care process assay or diagnostic process + creation date: 2018-11-27 + clinical data item + + + + + + + + + A health care encounter that is regularly scheduled for the purpose of health monitoring. + routine clinical visit + routine health care encounter + + + + + + + + + A health care encounter that is scheduled for the purpose of assessing a known set of specific issues + follow-up clinical visit + follow-up health care encounter + + + + + + + + + A congenital disorder arising as a result of an infectious process + congenital infection + + + + + + + + + A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality + drug induced congenital malformation + + + + + + + + + A pathological bodily process that occurs in the fetus during fetal development + congenital process + + + + + + + + + An abnormal material entity that is part of a patient and hypothesized to be clinically relevant. + Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension + physical sign + + + + + + + + + The process in which an allergic disease unfolds. + allergic disease process + + + + + + + + + The process in which cancer unfolds + cancer process + + + + + + + + + The process in which an autoimmune disease unfolds. + autoimmune disease process + + + + + + + + + progression stage + + + + + + + + + cancer progression stage + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ). + cancer progression stage 0 + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass. + cancer progression stage I + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass. + cancer progression stage II + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes. + cancer progression stage III + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes. + cancer progression stage IV + + + + + + + + + The process in which an infectious disease unfolds + infectious disease process + + + + + + + + + An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant. + processual sign + + + + + + + + + An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant. + Example: the color of a rash; the shape of a melanoma + qualitative sign + + + + + + + + + A therapeutic procedure in which a body part is transferred into a organism + transplantation + + + + + + + + + A transplantation in which the body part is a non-fluid tissue + solid organ transplant + + + + + + + + + A transplantation in which the body part is a bodily fluid + transfusion + + + + + + + + + A disorder of some macroscopic part of a tissue + tissue disorder + + + + + + + + + A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass + neoplasm + + + + + + + + + A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease. + Originally OBIB_0000026 + medication role + + + + + + + + + A data item that is about a patient’s health that comes directly from the patient. A patient reported outcome can include subjective feelings regarding symptoms, functions in daily life, physical, mental, emotional, spiritual, and social well-being, and satisfaction with healthcare that has been received. + https://orcid.org/0000-0001-6378-1703 + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/patient-reported-outcome + https://orcid.org/0000-0001-9625-1899 + https://orcid.org/0000-0001-9990-8331 + https://orcid.org/0009-0003-7246-1252 + PRO + The outcome does not necessarily need to be related to a healthcare intervention. For example, it can be about a patient's overall quality of life related to a disease. + patient-reported outcome + + + + + - - root node + + + A data item about a persont's health status or condition resulting from healthcare interventions, treatments, or services. + https://orcid.org/0000-0001-6378-1703 + https://orcid.org/0000-0001-9990-8331 + https://orcid.org/0009-0003-7246-1252 + healthcare outcome report diff --git a/src/ontology/ogms-edit.owl b/src/ontology/ogms-edit.owl index 4c88ef8..b95e6d3 100644 --- a/src/ontology/ogms-edit.owl +++ b/src/ontology/ogms-edit.owl @@ -15,6 +15,7 @@ Prefix(oboInOwl:=) Ontology( Import() +Import() Import() Import() Import() @@ -604,7 +605,6 @@ SubClassOf(obo:OGMS_0000074 obo:BFO_0000031) # Class: obo:OGMS_0000077 (pathological formation) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000077 "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z") @@ -622,7 +622,6 @@ SubClassOf(obo:OGMS_0000078 obo:BFO_0000040) # Class: obo:OGMS_0000079 (portion of pathological body substance) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000079 "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z") @@ -649,7 +648,6 @@ SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061) # Class: obo:OGMS_0000082 (pathological invasion) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000082 "TODO: Define."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z") @@ -658,7 +656,6 @@ SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061) # Class: obo:OGMS_0000083 (physical examination finding) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000083 "TODO: Define."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z") AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding") @@ -804,7 +801,6 @@ SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096) # Class: obo:OGMS_0000099 (outpatient encounter) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000099 "TODO"@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z") AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter") diff --git a/src/ontology/ogms-odk.yaml b/src/ontology/ogms-odk.yaml index 68b582b..a85e8b5 100644 --- a/src/ontology/ogms-odk.yaml +++ b/src/ontology/ogms-odk.yaml @@ -43,6 +43,9 @@ import_group: - http://purl.obolibrary.org/obo/IDO_ - id: omo module_type: mirror + - id: cob + module_type: slme + slme_individuals: exclude use_custom_import_module: TRUE robot_java_args: '-Xmx8G' diff --git a/src/ontology/tmp/external_import_terms.txt b/src/ontology/tmp/external_import_terms.txt index 4ee8d51..769f45d 100644 --- a/src/ontology/tmp/external_import_terms.txt +++ b/src/ontology/tmp/external_import_terms.txt @@ -6,6 +6,7 @@ http://purl.obolibrary.org/obo/BFO_0000054 http://purl.obolibrary.org/obo/BFO_0000055 http://purl.obolibrary.org/obo/BFO_0000066 http://purl.obolibrary.org/obo/BFO_0000067 +http://purl.obolibrary.org/obo/COB_0000022 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000114 @@ -30,7 +31,6 @@ http://purl.obolibrary.org/obo/OBI_0000278 http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/OBI_0000846 http://purl.obolibrary.org/obo/OBI_0001688 -http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/OBI_0200000 http://purl.obolibrary.org/obo/OBI_0600052 http://purl.obolibrary.org/obo/RO_0000052 diff --git a/src/ontology/tmp/external_import_terms.txt.tmp b/src/ontology/tmp/external_import_terms.txt.tmp index dfcdad2..f39d814 100644 --- a/src/ontology/tmp/external_import_terms.txt.tmp +++ b/src/ontology/tmp/external_import_terms.txt.tmp @@ -11,7 +11,6 @@ http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/BFO_0000051 http://purl.obolibrary.org/obo/IDO_0000630 http://purl.obolibrary.org/obo/IAO_0000116 -http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/RO_0002083 http://purl.obolibrary.org/obo/RO_0002234 http://purl.obolibrary.org/obo/IAO_0000136 @@ -20,6 +19,7 @@ http://purl.obolibrary.org/obo/RO_0000056 http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.org/obo/BFO_0000055 +http://purl.obolibrary.org/obo/COB_0000022 http://purl.obolibrary.org/obo/RO_0002218 http://purl.obolibrary.org/obo/RO_0002353 http://purl.obolibrary.org/obo/IAO_0000600 diff --git a/src/ontology/tmp/merged-ogms-edit.ofn b/src/ontology/tmp/merged-ogms-edit.ofn index 77c2479..4f959b5 100644 --- a/src/ontology/tmp/merged-ogms-edit.ofn +++ b/src/ontology/tmp/merged-ogms-edit.ofn @@ -1,47 +1,1170 @@ Prefix(:=) -Prefix(dce:=) +Prefix(dc:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(foaf:=) +Prefix(rdf1:=) Prefix(rdfs:=) -Prefix(dcterms:=) +Prefix(terms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) Ontology( -Annotation(dcterms:description "None") -Annotation(dcterms:license ) -Annotation(dcterms:title "The Ontology for General Medical Science") - -Declaration(Class()) -Declaration(AnnotationProperty(dcterms:description)) -Declaration(AnnotationProperty(dcterms:license)) -Declaration(AnnotationProperty(dcterms:title)) +Annotation(dc:contributor "Matthew Diller"@en) +Annotation(dc:creator "Alan Ruttenberg") +Annotation(dc:creator "Albert Goldfain") +Annotation(dc:creator "Anand Kumar") +Annotation(dc:creator "Barry Smith") +Annotation(dc:creator "Bill Hogan") +Annotation(dc:creator "Brian Aevermann") +Annotation(dc:creator "Cornelius Rosse") +Annotation(dc:creator "Daniel Merico") +Annotation(dc:creator "Jie Zheng") +Annotation(dc:creator "Lindsay Cowell") +Annotation(dc:creator "Richard Scheuermann") +Annotation(dc:creator "Sivaram Arabandi") +Annotation(dc:creator "Werner Ceusters") +Annotation(dc:date "2009-08-07") +Annotation(dc:description "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. + +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."@en) +Annotation(dc:title "Ontology for General Medical Science") +Annotation(terms:license "http://creativecommons.org/licenses/by/4.0/") +Annotation(rdfs:comment "The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + +The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl + +The OGMS developer site is https://github.com/OGMS/ogms + +If you are interested in participating in the development of OGMS, please send email to matthew.diller@nih.gov"@en) + +Declaration(Class(obo:BFO_0000001)) +Declaration(Class(obo:BFO_0000015)) +Declaration(Class(obo:BFO_0000016)) +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:BFO_0000023)) +Declaration(Class(obo:BFO_0000031)) +Declaration(Class(obo:BFO_0000040)) +Declaration(Class(obo:IAO_0000027)) +Declaration(Class(obo:IAO_0000030)) +Declaration(Class(obo:OBI_0000011)) +Declaration(Class(obo:OBI_0000278)) +Declaration(Class(obo:OGMS_0000014)) +Declaration(Class(obo:OGMS_0000015)) +Declaration(Class(obo:OGMS_0000016)) +Declaration(Class(obo:OGMS_0000017)) +Declaration(Class(obo:OGMS_0000018)) +Declaration(Class(obo:OGMS_0000019)) +Declaration(Class(obo:OGMS_0000020)) +Declaration(Class(obo:OGMS_0000022)) +Declaration(Class(obo:OGMS_0000023)) +Declaration(Class(obo:OGMS_0000024)) +Declaration(Class(obo:OGMS_0000025)) +Declaration(Class(obo:OGMS_0000026)) +Declaration(Class(obo:OGMS_0000027)) +Declaration(Class(obo:OGMS_0000028)) +Declaration(Class(obo:OGMS_0000029)) +Declaration(Class(obo:OGMS_0000030)) +Declaration(Class(obo:OGMS_0000031)) +Declaration(Class(obo:OGMS_0000032)) +Declaration(Class(obo:OGMS_0000033)) +Declaration(Class(obo:OGMS_0000034)) +Declaration(Class(obo:OGMS_0000035)) +Declaration(Class(obo:OGMS_0000037)) +Declaration(Class(obo:OGMS_0000038)) +Declaration(Class(obo:OGMS_0000039)) +Declaration(Class(obo:OGMS_0000040)) +Declaration(Class(obo:OGMS_0000045)) +Declaration(Class(obo:OGMS_0000046)) +Declaration(Class(obo:OGMS_0000047)) +Declaration(Class(obo:OGMS_0000050)) +Declaration(Class(obo:OGMS_0000051)) +Declaration(Class(obo:OGMS_0000055)) +Declaration(Class(obo:OGMS_0000056)) +Declaration(Class(obo:OGMS_0000057)) +Declaration(Class(obo:OGMS_0000059)) +Declaration(Class(obo:OGMS_0000060)) +Declaration(Class(obo:OGMS_0000061)) +Declaration(Class(obo:OGMS_0000063)) +Declaration(Class(obo:OGMS_0000064)) +Declaration(Class(obo:OGMS_0000065)) +Declaration(Class(obo:OGMS_0000066)) +Declaration(Class(obo:OGMS_0000067)) +Declaration(Class(obo:OGMS_0000069)) +Declaration(Class(obo:OGMS_0000070)) +Declaration(Class(obo:OGMS_0000071)) +Declaration(Class(obo:OGMS_0000073)) +Declaration(Class(obo:OGMS_0000074)) +Declaration(Class(obo:OGMS_0000077)) +Declaration(Class(obo:OGMS_0000078)) +Declaration(Class(obo:OGMS_0000079)) +Declaration(Class(obo:OGMS_0000080)) +Declaration(Class(obo:OGMS_0000081)) +Declaration(Class(obo:OGMS_0000082)) +Declaration(Class(obo:OGMS_0000083)) +Declaration(Class(obo:OGMS_0000084)) +Declaration(Class(obo:OGMS_0000085)) +Declaration(Class(obo:OGMS_0000086)) +Declaration(Class(obo:OGMS_0000087)) +Declaration(Class(obo:OGMS_0000088)) +Declaration(Class(obo:OGMS_0000089)) +Declaration(Class(obo:OGMS_0000090)) +Declaration(Class(obo:OGMS_0000091)) +Declaration(Class(obo:OGMS_0000092)) +Declaration(Class(obo:OGMS_0000093)) +Declaration(Class(obo:OGMS_0000094)) +Declaration(Class(obo:OGMS_0000095)) +Declaration(Class(obo:OGMS_0000096)) +Declaration(Class(obo:OGMS_0000097)) +Declaration(Class(obo:OGMS_0000098)) +Declaration(Class(obo:OGMS_0000099)) +Declaration(Class(obo:OGMS_0000100)) +Declaration(Class(obo:OGMS_0000101)) +Declaration(Class(obo:OGMS_0000102)) +Declaration(Class(obo:OGMS_0000103)) +Declaration(Class(obo:OGMS_0000104)) +Declaration(Class(obo:OGMS_0000105)) +Declaration(Class(obo:OGMS_0000106)) +Declaration(Class(obo:OGMS_0000107)) +Declaration(Class(obo:OGMS_0000108)) +Declaration(Class(obo:OGMS_0000109)) +Declaration(Class(obo:OGMS_0000110)) +Declaration(Class(obo:OGMS_0000111)) +Declaration(Class(obo:OGMS_0000112)) +Declaration(Class(obo:OGMS_0000113)) +Declaration(Class(obo:OGMS_0000114)) +Declaration(Class(obo:OGMS_0000115)) +Declaration(Class(obo:OGMS_0000116)) +Declaration(Class(obo:OGMS_0000117)) +Declaration(Class(obo:OGMS_0000118)) +Declaration(Class(obo:OGMS_0000119)) +Declaration(Class(obo:OGMS_0000120)) +Declaration(Class(obo:OGMS_0000121)) +Declaration(Class(obo:OGMS_0000122)) +Declaration(Class(obo:OGMS_0000123)) +Declaration(Class(obo:OGMS_0000124)) +Declaration(Class(obo:OGMS_0000125)) +Declaration(Class(obo:OGMS_0000126)) +Declaration(Class(obo:OGMS_0000127)) +Declaration(Class(obo:OGMS_0000128)) +Declaration(Class(obo:OGMS_0000129)) +Declaration(Class(obo:OGMS_0000130)) +Declaration(Class(obo:OGMS_0000131)) +Declaration(Class(obo:OGMS_0000132)) +Declaration(Class(obo:OGMS_0000133)) +Declaration(Class(obo:OGMS_0000134)) +Declaration(Class(obo:OGMS_0000135)) +Declaration(Class(obo:OGMS_0000136)) +Declaration(Class(obo:OGMS_0000137)) +Declaration(Class(obo:OGMS_0000138)) +Declaration(Class(obo:OGMS_0000139)) +Declaration(Class(obo:OGMS_0000140)) +Declaration(Class(obo:OGMS_0000141)) +Declaration(Class(obo:OGMS_0000142)) +Declaration(Class(obo:OGMS_0000143)) +Declaration(Class(obo:OGMS_0000144)) +Declaration(Class(obo:OGMS_0000145)) +Declaration(Class(obo:OGMS_0000146)) +Declaration(Class(obo:OGMS_0000147)) +Declaration(Class(obo:OGMS_0000148)) +Declaration(Class(obo:OGMS_0000149)) +Declaration(Class(obo:OGMS_0000150)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000116)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(obo:IAO_0000119)) +Declaration(AnnotationProperty(obo:IAO_0000232)) +Declaration(AnnotationProperty(dc:contributor)) +Declaration(AnnotationProperty(dc:creator)) +Declaration(AnnotationProperty(dc:date)) +Declaration(AnnotationProperty(dc:description)) +Declaration(AnnotationProperty(dc:publisher)) +Declaration(AnnotationProperty(dc:title)) +Declaration(AnnotationProperty(terms:license)) +Declaration(AnnotationProperty(oboInOwl:hasBroadSynonym)) + + ############################ -# Annotation Properties +# Classes ############################ -# Annotation Property: dcterms:description (description) +# Class: obo:OGMS_0000014 (clinical finding) -AnnotationAssertion(rdfs:label dcterms:description "description") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000014 "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000014 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000014 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000014 "creation date: 2010-07-19T10:18:02Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000014 "clinical finding") +SubClassOf(obo:OGMS_0000014 obo:OGMS_0000123) -# Annotation Property: dcterms:license (license) +# Class: obo:OGMS_0000015 (clinical history) -AnnotationAssertion(rdfs:label dcterms:license "license") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000015 "A series of statements representing health-relevant qualities of a patient and of a patient's family."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000015 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000015 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000015 "creation date: 2010-07-19T10:18:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000015 "clinical history") +SubClassOf(obo:OGMS_0000015 obo:OGMS_0000123) -# Annotation Property: dcterms:title (title) +# Class: obo:OGMS_0000016 (clinical picture) -AnnotationAssertion(rdfs:label dcterms:title "title") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000016 "A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000016 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000016 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000016 "creation date: 2010-07-19T10:20:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000016 "clinical picture") +SubClassOf(obo:OGMS_0000016 obo:OGMS_0000123) +# Class: obo:OGMS_0000017 (clinical finding from image) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000017 "An interpretation of an image that is the output of a clinical evaluation and supports an inference to an assertion about some quality of a patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000017 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000017 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000017 "creation date: 2009-06-23T10:21:10Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000017 "clinical finding from image"@en) +SubClassOf(obo:OGMS_0000017 obo:OGMS_0000014) -############################ -# Classes -############################ +# Class: obo:OGMS_0000018 (laboratory finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000018 "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000018 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000018 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000018 "creation date: 2009-06-23T10:21:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000018 "laboratory finding") +SubClassOf(obo:OGMS_0000018 obo:OGMS_0000014) + +# Class: obo:OGMS_0000019 (preclinical finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000019 "A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000019 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000019 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000019 "creation date: 2009-06-23T10:22:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000019 "preclinical finding") +SubClassOf(obo:OGMS_0000019 obo:IAO_0000027) + +# Class: obo:OGMS_0000020 (symptom) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000020 "A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000020 "note: defined class") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000020 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000020 "creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06") +AnnotationAssertion(rdfs:label obo:OGMS_0000020 "symptom") +SubClassOf(obo:OGMS_0000020 obo:BFO_0000015) + +# Class: obo:OGMS_0000022 (manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000022 "A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000022 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000022 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000022 "creation date: 2009-06-23T11:12:33Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000022 "manifestation of a disease") +SubClassOf(obo:OGMS_0000022 obo:BFO_0000019) + +# Class: obo:OGMS_0000023 (phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000023 "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000023 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000023 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000023 "creation date: 2010-07-19T11:13:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000023 "phenotype") +SubClassOf(obo:OGMS_0000023 obo:BFO_0000019) + +# Class: obo:OGMS_0000024 (obsolete_sign) + +AnnotationAssertion(rdfs:comment obo:OGMS_0000024 "The class sign has been replaced by three seperate classes which reflect the different types of signs possible.") +AnnotationAssertion(rdfs:label obo:OGMS_0000024 "obsolete_sign") +AnnotationAssertion(owl:deprecated obo:OGMS_0000024 "true"^^xsd:boolean) + +# Class: obo:OGMS_0000025 (clinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000025 "A manifestation of a disease that is detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000025 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000025 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000025 "creation date: 2009-06-23T11:15:43Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000025 "clinical manifestation of a disease") +SubClassOf(obo:OGMS_0000025 obo:OGMS_0000022) + +# Class: obo:OGMS_0000026 (preclinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000026 "A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000026 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000026 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000026 "creation date: 2009-06-23T11:16:50Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000026 "preclinical manifestation of a disease") +SubClassOf(obo:OGMS_0000026 obo:OGMS_0000022) + +# Class: obo:OGMS_0000027 (clinical phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000027 "A clinically abnormal phenotype."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000027 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000027 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000027 "creation date: 2009-06-23T11:18:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000027 "clinical phenotype") +SubClassOf(obo:OGMS_0000027 obo:OGMS_0000023) + +# Class: obo:OGMS_0000028 (disease phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000028 "A clinically abnormal phenotype that is characteristic of a single disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000028 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000028 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000028 "creation date: 2009-06-23T11:18:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000028 "disease phenotype") +SubClassOf(obo:OGMS_0000028 obo:OGMS_0000023) + +# Class: obo:OGMS_0000029 (vital sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000029 "A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000029 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000029 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000029 "creation date: 2009-06-23T11:19:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000029 "vital sign") +SubClassOf(obo:OGMS_0000029 obo:OGMS_0000129) + +# Class: obo:OGMS_0000030 (predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000030 "A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000030 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000030 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000030 "creation date: 2009-06-23T11:20:25Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000030 "predisposition to disease of type X") +SubClassOf(obo:OGMS_0000030 obo:BFO_0000016) + +# Class: obo:OGMS_0000031 (disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000031 "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000031 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000031 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000031 "creation date: 2009-06-23T11:21:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000031 "disease") +SubClassOf(obo:OGMS_0000031 obo:BFO_0000016) + +# Class: obo:OGMS_0000032 (homeostasis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000032 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000032 "creation date: 2009-06-23T11:22:01Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000032 "homeostasis") +SubClassOf(obo:OGMS_0000032 obo:BFO_0000016) + +# Class: obo:OGMS_0000033 (genetic predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000033 "A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000033 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000033 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000033 "creation date: 2009-06-23T11:23:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000033 "genetic predisposition to disease of type X") +SubClassOf(obo:OGMS_0000033 obo:OGMS_0000030) + +# Class: obo:OGMS_0000034 (acquired genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000034 "A disease whose physical basis is an acquired genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000034 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000034 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000034 "creation date: 2009-06-23T11:24:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000034 "acquired genetic disease") +SubClassOf(obo:OGMS_0000034 obo:OGMS_0000031) + +# Class: obo:OGMS_0000035 (constitutional genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000035 "A disease whose physical basis is a constitutional genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000035 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000035 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000035 "creation date: 2009-06-23T11:24:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000035 "constitutional genetic disease") +SubClassOf(obo:OGMS_0000035 obo:OGMS_0000031) + +# Class: obo:OGMS_0000037 (altered homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000037 "Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000037 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000037 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000037 "creation date: 2009-06-23T11:26:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000037 "altered homeostasis") +SubClassOf(obo:OGMS_0000037 obo:OGMS_0000032) + +# Class: obo:OGMS_0000038 (normal homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000038 "Homeostasis of a type that is not clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000038 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000038 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000038 "creation date: 2009-06-23T11:27:28Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000038 "normal homeostasis") +SubClassOf(obo:OGMS_0000038 obo:OGMS_0000032) + +# Class: obo:OGMS_0000039 (configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000039 "A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000039 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000039 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000039 "creation date: 2009-06-23T11:36:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000039 "configuration") +SubClassOf(obo:OGMS_0000039 obo:BFO_0000019) + +# Class: obo:OGMS_0000040 (pathological physical configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000040 "A configuration which deviates in some way from a canonical configuration for a particular organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000040 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000040 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000040 "creation date: 2009-06-23T11:36:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000040 "pathological physical configuration") +SubClassOf(obo:OGMS_0000040 obo:OGMS_0000039) + +# Class: obo:OGMS_0000045 (disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000045 "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000045 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000045 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000045 "creation date: 2009-06-23T11:39:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000045 "disorder") +SubClassOf(obo:OGMS_0000045 obo:BFO_0000040) + +# Class: obo:OGMS_0000046 (epigenetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000046 "A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000046 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000046 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000046 "creation date: 2009-06-23T11:40:27Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000046 "epigenetic disorder") +SubClassOf(obo:OGMS_0000046 obo:OGMS_0000045) + +# Class: obo:OGMS_0000047 (genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000047 "A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000047 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000047 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000047 "creation date: 2009-06-23T11:41:14Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000047 "genetic disorder") +SubClassOf(obo:OGMS_0000047 obo:OGMS_0000045) + +# Class: obo:OGMS_0000050 (acquired genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000050 "A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000050 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000050 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000050 "creation date: 2009-06-23T11:43:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000050 "acquired genetic disorder") +SubClassOf(obo:OGMS_0000050 obo:OGMS_0000047) + +# Class: obo:OGMS_0000051 (constitutional genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000051 "A genetic disorder inherited during conception that is part of all cells in the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000051 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000051 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000051 "creation date: 2009-06-23T11:43:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000051 "constitutional genetic disorder") +SubClassOf(obo:OGMS_0000051 obo:OGMS_0000047) + +# Class: obo:OGMS_0000055 (clinical history taking) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000055 "A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000055 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000055 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000055 "creation date: 2009-06-23T11:49:16Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000055 "clinical history taking") +SubClassOf(obo:OGMS_0000055 obo:OGMS_0000108) + +# Class: obo:OGMS_0000056 (clinical laboratory test) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000056 "A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000056 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000056 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000056 "creation date: 2009-06-23T11:49:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000056 "clinical laboratory test") +SubClassOf(obo:OGMS_0000056 obo:OGMS_0000108) + +# Class: obo:OGMS_0000057 (physical examination) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000057 "A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000057 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000057 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000057 "creation date: 2010-07-19T11:50:18Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000057 "physical examination") +SubClassOf(obo:OGMS_0000057 obo:OGMS_0000108) + +# Class: obo:OGMS_0000059 (etiological process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000059 "A process in an organism that leads to a subsequent disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000059 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000059 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000059 "creation date: 2009-06-23T11:53:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000059 "etiological process") +SubClassOf(obo:OGMS_0000059 obo:BFO_0000015) + +# Class: obo:OGMS_0000060 (bodily process) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000060 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000060 "creation date: 2009-06-23T11:53:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000060 "bodily process") +SubClassOf(obo:OGMS_0000060 obo:BFO_0000015) + +# Class: obo:OGMS_0000061 (pathological bodily process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000061 "A bodily process that is clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000061 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000061 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000061 "creation date: 2009-06-23T11:54:29Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000061 "pathological bodily process") +SubClassOf(obo:OGMS_0000061 obo:OGMS_0000060) + +# Class: obo:OGMS_0000063 (disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000063 "The totality of all processes through which a given disease instance is realized."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000063 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000063 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000063 "creation date: 2009-06-23T11:55:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000063 "disease course") +SubClassOf(obo:OGMS_0000063 obo:BFO_0000015) + +# Class: obo:OGMS_0000064 (chronic disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000064 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000064 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000064 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000064 "creation date: 2009-06-23T11:56:26Z + +10212020 + +for definition use: +http://purl.obolibrary.org/obo/PATO_0001863") +AnnotationAssertion(rdfs:label obo:OGMS_0000064 "chronic disease course") +SubClassOf(obo:OGMS_0000064 obo:OGMS_0000063) + +# Class: obo:OGMS_0000065 (progressive disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000065 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000065 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000065 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000065 "creation date: 2009-06-23T11:57:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000065 "progressive disease course") +SubClassOf(obo:OGMS_0000065 obo:OGMS_0000063) + +# Class: obo:OGMS_0000066 (transient disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000066 "A disease course that terminates in a return to normal homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000066 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000066 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000066 "creation date: 2009-06-23T11:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000066 "transient disease course") +SubClassOf(obo:OGMS_0000066 obo:OGMS_0000063) + +# Class: obo:OGMS_0000067 (_undefined primitive term) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000067 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000067 "creation date: 2009-06-23T11:58:22Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000067 "_undefined primitive term") +SubClassOf(obo:OGMS_0000067 obo:BFO_0000001) + +# Class: obo:OGMS_0000069 (clinically abnormal) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000069 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000069 "creation date: 2009-06-23T11:59:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000069 "clinically abnormal") +SubClassOf(obo:OGMS_0000069 obo:OGMS_0000067) + +# Class: obo:OGMS_0000070 (physical basis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000070 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000070 "creation date: 2009-06-23T12:00:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000070 "physical basis") +SubClassOf(obo:OGMS_0000070 obo:OGMS_0000067) + +# Class: obo:OGMS_0000071 (realization) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000071 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000071 "creation date: 2009-06-23T12:00:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000071 "realization") +SubClassOf(obo:OGMS_0000071 obo:OGMS_0000067) + +# Class: obo:OGMS_0000073 (diagnosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000073 "The representation of a conclusion of a diagnostic process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000073 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000073 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000073 "creation date: 2009-06-23T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000073 "diagnosis") +SubClassOf(obo:OGMS_0000073 obo:OGMS_0000123) + +# Class: obo:OGMS_0000074 (normal value) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000074 "A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000074 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000074 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000074 "creation date: 2009-06-26T10:31:34Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000074 "normal value") +SubClassOf(obo:OGMS_0000074 obo:BFO_0000031) + +# Class: obo:OGMS_0000077 (pathological formation) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000077 "pathological formation") +SubClassOf(obo:OGMS_0000077 obo:BFO_0000040) + +# Class: obo:OGMS_0000078 (pathological anatomical structure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000078 "An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000078 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000078 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000078 "creation date: 2009-07-13T02:14:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000078 "pathological anatomical structure") +SubClassOf(obo:OGMS_0000078 obo:BFO_0000040) + +# Class: obo:OGMS_0000079 (portion of pathological body substance) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000079 "portion of pathological body substance") +SubClassOf(obo:OGMS_0000079 obo:BFO_0000040) + +# Class: obo:OGMS_0000080 (pathological transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000080 "A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000080 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000080 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000080 "creation date: 2009-07-13T02:17:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000080 "pathological transformation") +SubClassOf(obo:OGMS_0000080 obo:OGMS_0000061) + +# Class: obo:OGMS_0000081 (pathological derivation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000081 "A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000081 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000081 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000081 "creation date: 2009-07-13T02:17:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000081 "pathological derivation") +SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061) + +# Class: obo:OGMS_0000082 (pathological invasion) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000082 "pathological invasion") +SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061) + +# Class: obo:OGMS_0000083 (physical examination finding) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding") +SubClassOf(obo:OGMS_0000083 obo:OGMS_0000014) + +# Class: obo:OGMS_0000084 (organism population) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000084 "An aggregate of organisms of the same type."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000084 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000084 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000084 "organism population") +SubClassOf(obo:OGMS_0000084 obo:BFO_0000040) + +# Class: obo:OGMS_0000085 (pain) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000085 "A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000085 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000085 "https://philarchive.org/rec/SMITAO-12") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000085 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000085 "pain") +SubClassOf(obo:OGMS_0000085 obo:OGMS_0000020) + +# Class: obo:OGMS_0000086 (syndrome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000086 "A pattern of signs and symptoms that typically co-occur."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000086 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000086 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000086 "syndrome") +SubClassOf(obo:OGMS_0000086 obo:BFO_0000019) + +# Class: obo:OGMS_0000087 (extended organism) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000087 "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000087 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000087 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000087 "extended organism") +SubClassOf(obo:OGMS_0000087 obo:BFO_0000040) + +# Class: obo:OGMS_0000088 (patient symptom report) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000088 "A communication from a patient about something they perceive as being abnormal about their body or life."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000088 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000088 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000088 "patient symptom report") +SubClassOf(obo:OGMS_0000088 obo:IAO_0000030) + +# Class: obo:OGMS_0000089 (congenital disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000089 "A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000089 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000089 "congenital malformation") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000089 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000089 "congenital disorder") +SubClassOf(obo:OGMS_0000089 obo:BFO_0000040) + +# Class: obo:OGMS_0000090 (treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000090 "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000090 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000090 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000090 "treatment") +SubClassOf(obo:OGMS_0000090 obo:OGMS_0000096) + +# Class: obo:OGMS_0000091 (convalescence) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000091 "A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000091 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000091 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000091 "convalescence") +SubClassOf(obo:OGMS_0000091 obo:BFO_0000015) + +# Class: obo:OGMS_0000092 (life course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000092 "A process which has as parts all the processes in which a given organism is participant."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000092 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000092 "creation date: 2010-03-31T04:51:11Z + +EDIT: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000092 "life course") +SubClassOf(obo:OGMS_0000092 obo:BFO_0000015) + +# Class: obo:OGMS_0000093 (prognosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000093 "A hypothesis about some future part of a disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000093 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000093 "creation date: 2010-03-31T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000093 "prognosis") +SubClassOf(obo:OGMS_0000093 obo:IAO_0000027) + +# Class: obo:OGMS_0000094 (acute disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000094 "A disease course with an acute onset"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000094 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000094 "creation date: 2010-07-19T11:57:44Z + +10212020 + +for definition use + +http://purl.obolibrary.org/obo/PATO_0000389") +AnnotationAssertion(rdfs:label obo:OGMS_0000094 "acute disease course") +SubClassOf(obo:OGMS_0000094 obo:OGMS_0000063) + +# Class: obo:OGMS_0000095 (inflammatory process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000095 "A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000095 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000095 "creation date: 2010-07-19T11:57:44Z + +Updated: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000095 "inflammatory process") +SubClassOf(obo:OGMS_0000095 obo:OGMS_0000060) + +# Class: obo:OGMS_0000096 (health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000096 "A planned process with the objective to improve or maintain the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000096 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000096 "creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18") +AnnotationAssertion(rdfs:label obo:OGMS_0000096 "health care process") +SubClassOf(obo:OGMS_0000096 obo:OBI_0000011) + +# Class: obo:OGMS_0000097 (health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000097 "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000097 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000097 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000097 "health care encounter") +SubClassOf(obo:OGMS_0000097 obo:OGMS_0000096) + +# Class: obo:OGMS_0000098 (hospitalization) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000098 "A health care process in which a person is admitted to a hospital for treatment, diagnosis, or monitoring."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000098 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000098 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000098 "hospitalization") +SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096) + +# Class: obo:OGMS_0000099 (outpatient encounter) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter") +SubClassOf(obo:OGMS_0000099 obo:OGMS_0000097) + +# Class: obo:OGMS_0000100 (inpatient encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000100 "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000100 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000100 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000100 "inpatient encounter") +SubClassOf(obo:OGMS_0000100 obo:OGMS_0000097) + +# Class: obo:OGMS_0000101 (emergency department encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000101 "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000101 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000101 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000101 "emergency department encounter") +SubClassOf(obo:OGMS_0000101 obo:OGMS_0000097) + +# Class: obo:OGMS_0000102 (injury) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000102 "A disorder that involves some structural damage that is immediately caused by a catastrophic external force."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000102 "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000102 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000102 "creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000102 "injury") +SubClassOf(obo:OGMS_0000102 obo:OGMS_0000045) + +# Class: obo:OGMS_0000103 (disease prophylaxis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000103 "A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000103 "Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000103 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000103 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000103 "disease prophylaxis") +SubClassOf(obo:OGMS_0000103 obo:OBI_0000011) + +# Class: obo:OGMS_0000104 (diagnostic process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000104 "A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000104 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000104 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000104 "diagnostic process") +SubClassOf(obo:OGMS_0000104 obo:OGMS_0000096) + +# Class: obo:OGMS_0000105 (relapse) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000105 "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000105 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000105 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000105 "recurrent") +AnnotationAssertion(dc:date obo:OGMS_0000105 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000105 "relapse"@en) +SubClassOf(obo:OGMS_0000105 obo:OBI_0000278) + +# Class: obo:OGMS_0000106 (remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000106 "A disease stage which is characterized by the lack of a manifestation of a disease") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000106 "A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000106 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(dc:date obo:OGMS_0000106 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000106 "remission"@en) +SubClassOf(obo:OGMS_0000106 obo:OBI_0000278) + +# Class: obo:OGMS_0000107 (ancillary health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000107 "A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient.") +AnnotationAssertion(dc:date obo:OGMS_0000107 "2017-04-18") +AnnotationAssertion(dc:publisher obo:OGMS_0000107 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000107 "ancillary health care process") +SubClassOf(obo:OGMS_0000107 obo:OBI_0000011) + +# Class: obo:OGMS_0000108 (health care process assay) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000108 "A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.") +AnnotationAssertion(dc:date obo:OGMS_0000108 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000108 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000108 "health care process assay") +SubClassOf(obo:OGMS_0000108 obo:OGMS_0000096) + +# Class: obo:OGMS_0000109 (health care process biomaterial transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000109 "A health care process which results in physical changes in a specified input material") +AnnotationAssertion(dc:date obo:OGMS_0000109 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000109 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000109 "health care process biomaterial transformation") +SubClassOf(obo:OGMS_0000109 obo:OGMS_0000096) + +# Class: obo:OGMS_0000110 (health care process data transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000110 "A health care process that produces output from input data") +AnnotationAssertion(dc:date obo:OGMS_0000110 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000110 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000110 "health care process data transformation") +SubClassOf(obo:OGMS_0000110 obo:OGMS_0000096) + +# Class: obo:OGMS_0000111 (prophylactic treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000111 "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000111 "Creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000111 "prophylactic treatment"@en) +SubClassOf(obo:OGMS_0000111 obo:OGMS_0000090) + +# Class: obo:OGMS_0000112 (therapeutic procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000112 "A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000112 "Creation data: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000112 "therapeutic procedure"@en) +SubClassOf(obo:OGMS_0000112 obo:OGMS_0000090) + +# Class: obo:OGMS_0000113 (chemotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000113 "A therapeutic procedure that uses synthetic or naturally-occurring chemicals") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000113 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000113 "chemotherapy procedure"@en) +SubClassOf(obo:OGMS_0000113 obo:OGMS_0000112) + +# Class: obo:OGMS_0000114 (immunotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000114 "A therapeutic procedure that uses immune system derived entities.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000114 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000114 "immunotherapy procedure"@en) +SubClassOf(obo:OGMS_0000114 obo:OGMS_0000112) + +# Class: obo:OGMS_0000115 (physical therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000115 "A therapeutic procedure that uses physical conditioning") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000115 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000115 "physical therapy procedure"@en) +SubClassOf(obo:OGMS_0000115 obo:OGMS_0000112) + +# Class: obo:OGMS_0000116 (radiation therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000116 "A therapeutic procedure that uses radiation.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000116 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000116 "radiation therapy procedure"@en) +SubClassOf(obo:OGMS_0000116 obo:OGMS_0000112) + +# Class: obo:OGMS_0000117 (asymptomatic) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000117 "A disease stage characterized by the lack of symptoms associated with a given disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000117 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000117 "asymptomatic"@en) +SubClassOf(obo:OGMS_0000117 obo:OBI_0000278) + +# Class: obo:OGMS_0000118 (onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000118 "A disease stage that marks the beginning of a disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000118 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000118 "onset"@en) +SubClassOf(obo:OGMS_0000118 obo:OBI_0000278) + +# Class: obo:OGMS_0000119 (acute onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000119 "A disease stage with a rapid unfolding of signs and symptoms") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000119 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000119 "acute onset"@en) +SubClassOf(obo:OGMS_0000119 obo:OGMS_0000118) + +# Class: obo:OGMS_0000120 (complete remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000120 "A remission which is characterized by a prolonged lack of all manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000120 "complete remission"@en) +SubClassOf(obo:OGMS_0000120 obo:OGMS_0000106) + +# Class: obo:OGMS_0000121 (partial remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000121 "A remission which is characterized by a prolonged lack of some manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000121 "partial remission"@en) +SubClassOf(obo:OGMS_0000121 obo:OGMS_0000106) + +# Class: obo:OGMS_0000122 (recovered from disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000122 "A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000122 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000122 "recovered from disease"@en) +SubClassOf(obo:OGMS_0000122 obo:BFO_0000019) + +# Class: obo:OGMS_0000123 (clinical data item) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000123 "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000123 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000123 "clinical data item"@en) +SubClassOf(obo:OGMS_0000123 obo:IAO_0000027) + +# Class: obo:OGMS_0000124 (routine health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000124 "A health care encounter that is regularly scheduled for the purpose of health monitoring.") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000124 "routine clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000124 "routine health care encounter") +SubClassOf(obo:OGMS_0000124 obo:OGMS_0000099) + +# Class: obo:OGMS_0000125 (follow-up health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000125 "A health care encounter that is scheduled for the purpose of assessing a known set of specific issues") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000125 "follow-up clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000125 "follow-up health care encounter") +SubClassOf(obo:OGMS_0000125 obo:OGMS_0000099) + +# Class: obo:OGMS_0000126 (congenital infection) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000126 "A congenital disorder arising as a result of an infectious process") +AnnotationAssertion(rdfs:label obo:OGMS_0000126 "congenital infection") +SubClassOf(obo:OGMS_0000126 obo:OGMS_0000089) + +# Class: obo:OGMS_0000127 (drug induced congenital malformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000127 "A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality") +AnnotationAssertion(rdfs:label obo:OGMS_0000127 "drug induced congenital malformation") +SubClassOf(obo:OGMS_0000127 obo:OGMS_0000089) + +# Class: obo:OGMS_0000128 (congenital process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000128 "A pathological bodily process that occurs in the fetus during fetal development") +AnnotationAssertion(rdfs:label obo:OGMS_0000128 "congenital process") +SubClassOf(obo:OGMS_0000128 obo:OGMS_0000061) + +# Class: obo:OGMS_0000129 (physical sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000129 "An abnormal material entity that is part of a patient and hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000129 "Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension") +AnnotationAssertion(rdfs:label obo:OGMS_0000129 "physical sign") +SubClassOf(obo:OGMS_0000129 obo:BFO_0000040) + +# Class: obo:OGMS_0000130 (allergic disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000130 "The process in which an allergic disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000130 "allergic disease process") +SubClassOf(obo:OGMS_0000130 obo:OGMS_0000061) + +# Class: obo:OGMS_0000131 (cancer process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000131 "The process in which cancer unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000131 "cancer process") +SubClassOf(obo:OGMS_0000131 obo:OGMS_0000061) + +# Class: obo:OGMS_0000132 (autoimmune disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000132 "The process in which an autoimmune disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000132 "autoimmune disease process") +SubClassOf(obo:OGMS_0000132 obo:OGMS_0000061) + +# Class: obo:OGMS_0000133 (progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000133 "progression stage") +SubClassOf(obo:OGMS_0000133 obo:OBI_0000278) + +# Class: obo:OGMS_0000134 (cancer progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000134 "cancer progression stage") +SubClassOf(obo:OGMS_0000134 obo:OGMS_0000133) + +# Class: obo:OGMS_0000135 (cancer progression stage 0) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000135 "A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ).") +AnnotationAssertion(rdfs:label obo:OGMS_0000135 "cancer progression stage 0") +SubClassOf(obo:OGMS_0000135 obo:OGMS_0000134) + +# Class: obo:OGMS_0000136 (cancer progression stage I) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000136 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000136 "cancer progression stage I") +SubClassOf(obo:OGMS_0000136 obo:OGMS_0000134) + +# Class: obo:OGMS_0000137 (cancer progression stage II) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000137 "A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000137 "cancer progression stage II") +SubClassOf(obo:OGMS_0000137 obo:OGMS_0000134) + +# Class: obo:OGMS_0000138 (cancer progression stage III) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000138 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000138 "cancer progression stage III") +SubClassOf(obo:OGMS_0000138 obo:OGMS_0000134) + +# Class: obo:OGMS_0000139 (cancer progression stage IV) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000139 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000139 "cancer progression stage IV") +SubClassOf(obo:OGMS_0000139 obo:OGMS_0000134) + +# Class: obo:OGMS_0000140 (infectious disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000140 "The process in which an infectious disease unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000140 "infectious disease process") +SubClassOf(obo:OGMS_0000140 obo:OGMS_0000061) + +# Class: obo:OGMS_0000141 (processual sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000141 "An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(rdfs:label obo:OGMS_0000141 "processual sign") +SubClassOf(obo:OGMS_0000141 obo:BFO_0000015) + +# Class: obo:OGMS_0000142 (qualitative sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000142 "An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000142 "Example: the color of a rash; the shape of a melanoma") +AnnotationAssertion(rdfs:label obo:OGMS_0000142 "qualitative sign") +SubClassOf(obo:OGMS_0000142 obo:BFO_0000019) + +# Class: obo:OGMS_0000143 (transplantation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000143 "A therapeutic procedure in which a body part is transferred into a organism") +AnnotationAssertion(rdfs:label obo:OGMS_0000143 "transplantation") +SubClassOf(obo:OGMS_0000143 obo:OGMS_0000112) + +# Class: obo:OGMS_0000144 (solid organ transplant) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000144 "A transplantation in which the body part is a non-fluid tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000144 "solid organ transplant") +SubClassOf(obo:OGMS_0000144 obo:OGMS_0000143) + +# Class: obo:OGMS_0000145 (transfusion) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000145 "A transplantation in which the body part is a bodily fluid") +AnnotationAssertion(rdfs:label obo:OGMS_0000145 "transfusion") +SubClassOf(obo:OGMS_0000145 obo:OGMS_0000143) + +# Class: obo:OGMS_0000146 (tissue disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000146 "A disorder of some macroscopic part of a tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000146 "tissue disorder") +SubClassOf(obo:OGMS_0000146 obo:OGMS_0000045) + +# Class: obo:OGMS_0000147 (neoplasm) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000147 "A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass") +AnnotationAssertion(rdfs:label obo:OGMS_0000147 "neoplasm") +SubClassOf(obo:OGMS_0000147 obo:OGMS_0000146) + +# Class: obo:OGMS_0000148 (medication role) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000148 "A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000148 "Originally OBIB_0000026") +AnnotationAssertion(rdfs:label obo:OGMS_0000148 "medication role") +SubClassOf(obo:OGMS_0000148 obo:BFO_0000023) + +# Class: obo:OGMS_0000149 (patient-reported outcome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000149 "A data item that is about a patient’s health that comes directly from the patient. A patient reported outcome can include subjective feelings regarding symptoms, functions in daily life, physical, mental, emotional, spiritual, and social well-being, and satisfaction with healthcare that has been received."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000149 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000149 "https://www.cancer.gov/publications/dictionaries/cancer-terms/def/patient-reported-outcome") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(oboInOwl:hasBroadSynonym obo:OGMS_0000149 "PRO"@en) +AnnotationAssertion(rdfs:comment obo:OGMS_0000149 "The outcome does not necessarily need to be related to a healthcare intervention. For example, it can be about a patient's overall quality of life related to a disease."@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000149 "patient-reported outcome"@en) +SubClassOf(obo:OGMS_0000149 obo:IAO_0000027) -# Class: (root node) +# Class: obo:OGMS_0000150 (healthcare outcome report) -AnnotationAssertion(rdfs:label "root node"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000150 "A data item about a persont's health status or condition resulting from healthcare interventions, treatments, or services."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000150 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(rdfs:label obo:OGMS_0000150 "healthcare outcome report"@en) +SubClassOf(obo:OGMS_0000150 obo:IAO_0000027) ) \ No newline at end of file diff --git a/src/ontology/tmp/mirror-obi.owl b/src/ontology/tmp/mirror-obi.owl index 3478afb..5f39d3b 100644 --- a/src/ontology/tmp/mirror-obi.owl +++ b/src/ontology/tmp/mirror-obi.owl @@ -7,15 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -82,7 +79,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2025-05-01 + 2025-12-18 @@ -104,29 +101,6 @@ - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - @@ -138,7 +112,6 @@ The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred label editor preferred term editor preferred term @@ -155,7 +128,6 @@ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage @@ -216,7 +188,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition definition textual definition @@ -232,7 +203,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note @@ -247,7 +217,6 @@ We also have the outstanding issue of how to aim different definitions to differ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor @@ -263,9 +232,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - alternative term @@ -279,7 +246,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source @@ -304,7 +270,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note @@ -360,7 +325,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from @@ -509,7 +473,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation @@ -522,7 +485,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language - has associated axiom(nl) @@ -535,7 +497,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) @@ -600,7 +561,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label @@ -912,12 +872,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1051,12 +1005,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1185,6 +1133,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -1194,12 +1148,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1295,12 +1243,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1316,12 +1258,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1414,18 +1336,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - has part @@ -1434,18 +1346,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + realized in @@ -1456,13 +1358,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1471,15 +1367,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + preceded by @@ -1488,50 +1379,43 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + precedes - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + executed by + + + + + + + + intended to realize - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + has plan + + + + + + + + intended plan process type @@ -1551,6 +1435,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is about A (currently) primitive relation that relates an information artifact to an entity. @@ -1654,11 +1539,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has specified input see is_input_of example_of_usage - The inverse property of is specified input of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters @@ -1690,11 +1575,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of @@ -1743,10 +1628,10 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - + has specified output - The inverse property of is specified output of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter @@ -1910,10 +1795,10 @@ instance level relation [GOC:cjm] - + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of @@ -2011,7 +1896,7 @@ level of radioactivity is_proxy_for level of toxicity - + achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' @@ -2130,7 +2015,7 @@ level of radioactivity is_proxy_for level of toxicity - + objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. @@ -2255,15 +2140,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + - @@ -2377,15 +2262,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2394,16 +2271,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - has characteristic @@ -2412,15 +2280,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -2429,16 +2289,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2447,11 +2298,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as @@ -2461,10 +2307,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes @@ -2474,15 +2316,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this catalysis function is a function of this enzyme + function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of @@ -2491,14 +2327,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this red color is a quality of this apple + quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of @@ -2507,14 +2338,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this investigator role is a role of this person + role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of @@ -2523,13 +2349,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + has function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function + has function @@ -2538,12 +2360,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this apple has quality this red color + has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality + has quality @@ -2552,13 +2371,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) + has role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role + has role @@ -2567,11 +2382,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - + has disposition a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition @@ -2580,8 +2393,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + inverse of has disposition + disposition of @@ -2590,47 +2404,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - derives from - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - + derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from derives from - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -2640,97 +2425,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in + located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by @@ -2739,11 +2446,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes @@ -2752,14 +2456,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - + has component - @@ -2767,11 +2467,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - has function realized in - capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of @@ -2779,9 +2480,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - surrounded by - x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by @@ -2796,15 +2496,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + inverse of surrounded by + surrounds + + + + - - - move to BFO? - Allen - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation + temporally related to + + temporally related to @@ -2812,61 +2518,50 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + starts inverse of starts with - Chris Mungall - Allen + starts - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + has output - + - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true + + inverse of enables + enabled by - + - - DEPRECATED bearer of - true + + + has member + has member is a mereological relation between a collection and an item. + + has member @@ -2888,6 +2583,41 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + has quantity + + + + + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + @@ -2972,518 +2702,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - @@ -3491,226 +2715,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - @@ -3718,183 +2733,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - @@ -3902,105 +2742,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - site - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -4008,439 +2751,40 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - material - MaterialEntity + material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - + immaterial entity - + - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - @@ -4449,7 +2793,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ insulin - A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the β cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. insulin @@ -4459,7 +2803,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -4471,7 +2815,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -4491,7 +2835,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + An organic heterobicyclic compound that consists of 2-oxohexahydro-1<em>H</em>-thieno[3,4-<em>d</em>]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin @@ -4501,9 +2845,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3β-hydroxy group. cholesterol @@ -4513,7 +2857,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -4525,7 +2869,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -4537,7 +2881,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -4549,9 +2893,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + A one-carbon compound with formula CO<small><sub>2</sub></small> in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide @@ -4563,7 +2907,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide @@ -4573,7 +2917,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -4585,7 +2929,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -4597,9 +2941,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + A member of the class of 2-benzofurans that is 2-benzofuran-1(3<em>H</em>)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2<i>E</i>)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by <em>Penicillium brevi-compactum, P. stoloniferum, P. echinulatum</em> and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. mycophenolic acid @@ -4609,7 +2953,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -4621,7 +2965,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -4645,9 +2989,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + progesterone - A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + A C<small><sub>21</sub></small>-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. progesterone @@ -4657,7 +3001,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogensulfite hydrogensulfite @@ -4668,7 +3012,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -4680,7 +3024,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -4692,9 +3036,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + testosterone - An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + An androstanoid having 17β-hydroxy and 3-oxo groups, together with unsaturation at C-4‒C-5.. testosterone @@ -4704,9 +3048,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + A hemoprotein that is the ferric (Fe<small><sup>3+</small></sup>) form of hemoglobin. methemoglobin @@ -4716,7 +3060,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -4728,9 +3072,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. + A 17α-hydroxy-C<small><sub>21</sub></small>-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -4740,7 +3084,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -4752,7 +3096,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -4764,7 +3108,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -4776,7 +3120,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -4788,7 +3132,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -4797,23 +3141,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - molecular entity - - - - - + cytochalasin cytochalasin @@ -4824,7 +3155,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -4836,21 +3167,35 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + A member of the class of <em>N</em>-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea + + + + + hormone + Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. + + hormone + + + + - + + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton @@ -4860,7 +3205,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + iron cation iron cation @@ -4871,7 +3216,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -4883,7 +3228,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -4895,7 +3240,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -4907,7 +3252,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -4919,7 +3264,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lead(0) lead(0) @@ -4930,9 +3275,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + A complex glycopeptide from <em>Streptomyces orientalis</em>. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria <em>Staphylococcus aureus</em> and <em>Clostridium difficile</em>. vancomycin @@ -4944,7 +3289,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + A racemate comprising equimolar amounts of (<i>R</i>)- and (<i>S</i>)-lactic acid. rac-lactic acid @@ -4954,7 +3299,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -4966,9 +3311,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + An androstanoid that is androst-5-ene substituted by a β-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. dehydroepiandrosterone @@ -4978,7 +3323,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -4989,7 +3334,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -5001,7 +3346,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -5013,7 +3358,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -5025,7 +3370,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydroxyl hydroxyl @@ -5036,20 +3381,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek δευτερον, second). deuterium atom + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -5061,7 +3415,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ruthenium atom ruthenium atom @@ -5090,7 +3444,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -5102,7 +3456,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5114,9 +3468,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red @@ -5126,7 +3480,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -5138,7 +3492,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methyl group An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. @@ -5147,14 +3501,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus @@ -5162,7 +3522,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + elemental oxygen elemental oxygen @@ -5173,7 +3533,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rare earth metal atom rare earth metal atom @@ -5184,7 +3544,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -5196,7 +3556,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium atom gadolinium atom @@ -5207,7 +3567,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + terbium atom terbium atom @@ -5220,7 +3580,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), <small>D</small>-ribose or 2-deoxy-<small>D</small>-ribose and phosphoric acid. nucleic acid @@ -5242,7 +3602,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amino acid A carboxylic acid containing one or more amino groups. @@ -5254,7 +3614,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer @@ -5267,7 +3627,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hemoglobin hemoglobin @@ -5278,7 +3638,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -5290,7 +3650,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium molecular entity gadolinium molecular entity @@ -5301,7 +3661,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -5310,10 +3670,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A particle smaller than an atom. + subatomic particle + + + + - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5325,9 +3696,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more <small>L</small>-glutamic acid units. folic acids @@ -5337,7 +3708,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium phosphate sodium phosphate @@ -5348,7 +3719,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5367,7 +3738,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5376,7 +3747,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin <small><sup>1</small></sup>/<small><sub>2</sub></small>. phosphorus-33 atom @@ -5456,7 +3827,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5467,7 +3838,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium ion calcium ion @@ -5478,7 +3849,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + magnesium cation Any magnesium ion that is positively charged. @@ -5510,7 +3881,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + A hydroxy steroid that consists of 5β-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3β-, 12β- and 14β-positions. It has been isolated from the plant species of the genus <em>Digitalis</em>. digoxigenin @@ -5520,7 +3891,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -5532,7 +3903,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + deoxyribonucleotide A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. @@ -5544,9 +3915,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + A cardenolide glycoside that is digitoxin β-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, <em>Digitalis lanata</em>, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. digoxin @@ -5567,7 +3938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -5579,7 +3950,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -5591,7 +3962,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -5603,15 +3974,26 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of γ rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 + + + + + resorufin + + resorufin + + + + @@ -5667,7 +4049,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -5679,7 +4061,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -5691,7 +4073,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -5703,7 +4085,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -5715,9 +4097,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two <em>N</em>-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5727,9 +4109,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent. N-methylisatoic anhydride @@ -5739,9 +4121,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (<i>S</i>)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5751,7 +4133,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -5763,9 +4145,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue @@ -5775,7 +4157,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -5787,7 +4169,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -5799,7 +4181,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -5811,7 +4193,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + thyroid stimulating hormone thyroid stimulating hormone @@ -5822,7 +4204,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Luteinizing hormone Luteinizing hormone @@ -5833,7 +4215,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Follicle stimulating hormone Follicle stimulating hormone @@ -5844,9 +4226,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + A hydroxycalciol that is vitamin D<small><sub>2</sub></small> in which the hydrogen at position 25 has been replaced by a hydroxy group. 25-hydroxyvitamin D2 @@ -5856,9 +4238,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + A primary amino compound that is <em>tert</em>-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7—9; p<em>K</em><small><sub>a</sub></small> = 8.3 at 20 °C; p<em>K</em><small><sub>a</sub></small> = 7.82 at 37 °C. tris @@ -5980,24 +4362,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + + cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. cell line cell - - - - - - - - - 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. - @@ -6109,10 +4487,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell @@ -6276,6 +4656,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte + A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. + + oligodendrocyte + + + + @@ -6437,11 +4829,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + experimentally modified cell in vitro @@ -6612,10 +5003,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mononuclear cell + mononuclear leukocyte A leukocyte with a single non-segmented nucleus in the mature form. - mononuclear cell + mononuclear leukocyte @@ -6692,14 +5083,297 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + - complex of molecules - A complex of two or more molecular entities that are not covalently bound. - - complex of molecules + + + + + + + A complex of two or more molecules that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A completely executed planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device @@ -6740,6 +5414,36 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental system process + + + + @@ -7014,7 +5718,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -7205,7 +5911,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RNA nuclease activity - Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + Catalysis of the cleavage of phosphodiester bonds in chains of RNA. RNA nuclease activity @@ -7227,6 +5933,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). @@ -7296,6 +6011,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of DNA repair + Any process that modulates the frequency, rate or extent of DNA repair. + + regulation of DNA repair + + + + @@ -7320,6 +6047,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + apoptotic process + A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. + + apoptotic process + + + + @@ -7344,6 +6083,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + plasma membrane organization + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + + plasma membrane organization + + + + @@ -7368,6 +6119,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryo implantation + Attachment of the blastocyst to the uterine lining. + + embryo implantation + + + + @@ -7396,10 +6159,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + + biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological process biological_process @@ -7549,6 +6318,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oxidoreductase activity + Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. + + oxidoreductase activity + + + + @@ -7585,6 +6366,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytolysis + The rupture of cell membranes and the loss of cytoplasm. + + cytolysis + + + + @@ -7669,6 +6462,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron differentiation + The process in which a relatively unspecialized cell acquires specialized features of a neuron. + + neuron differentiation + + + + + + + + + neuron projection development + The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). + + neuron projection development + + + + @@ -8190,7 +7007,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + @@ -8200,6 +7018,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. protein complex protein-containing complex @@ -8375,6 +7194,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hormone biosynthetic process + The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone biosynthetic process + + + + + + + + + hormone catabolic process + The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone catabolic process + + + + @@ -8439,6 +7282,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron projection + A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. + + neuron projection + + + + @@ -8475,6 +7330,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + @@ -8511,6 +7376,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + DNA-templated DNA replication maintenance of fidelity + A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair. + + DNA-templated DNA replication maintenance of fidelity + + + + @@ -8523,6 +7400,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synapse + The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. + + synapse + + + + @@ -8535,6 +7424,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte differentiation + The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. + + oligodendrocyte differentiation + + + + + + + + + anatomical structure development + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. + + anatomical structure development + + + + @@ -8607,6 +7520,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryonic process involved in female pregnancy + A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. + + embryonic process involved in female pregnancy + + + + + + + + + estrous cycle phase + The progression of physiological phases, occurring in the endometrium during the estrous cycle that recur at regular intervals during the reproductive years. The estrous cycle is an ovulation cycle where the endometrium is resorbed if pregnancy does not occur. + + estrous cycle phase + + + + @@ -8835,6 +7772,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of synapse maturation + Any process that modulates the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state. + + regulation of synapse maturation + + + + @@ -8967,6 +7916,37 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + neuron projection arborization + The process in which the anatomical structures of a neuron projection are generated and organized into branches. A neuron projection is any process extending from a neural cell, such as axons or dendrites. + + neuron projection arborization + + + + @@ -8991,6 +7971,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + mitotic DNA replication maintenance of fidelity + Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication. + + mitotic DNA replication maintenance of fidelity + + + + @@ -9015,6 +8007,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Severity + The intensity or degree of a manifestation. + + Severity + + + + @@ -9063,6 +8067,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + @@ -9116,9 +8130,10 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. + Pier: 'data, information or knowledge'. OR 'representation' information content entity @@ -9625,7 +8640,7 @@ clustering algorithm. - + documenting A planned process in which a document is created or added to by including the specified input in it. @@ -9650,7 +8665,7 @@ points together with a line. - + assigning a centrally registered identifier A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity @@ -10021,6 +9036,17 @@ No imports + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + @@ -10415,7 +9441,7 @@ No imports - + Viruses Viruses @@ -10560,10 +9586,19 @@ No imports + + + + + cellular organism + + + + - + Treponema pallidum Treponema pallidum @@ -10585,7 +9620,7 @@ No imports - + Bacteria eubacteria @@ -10597,7 +9632,7 @@ No imports - + Archaea Archaea @@ -10644,7 +9679,7 @@ No imports - + Eukaryota eucaryotes eukaryotes @@ -10753,6 +9788,17 @@ No imports + + + + + Pseudomonadati + + Pseudomonadati + + + + @@ -10982,7 +10028,7 @@ No imports - + Orientia tsutsugamushi Orientia tsutsugamushi @@ -11060,7 +10106,7 @@ No imports - + biological attribute biological attribute @@ -11223,30 +10269,21 @@ No imports - - - - - - - - - - - - - planned process + + obsolete planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + obsolete planned process + true @@ -11529,7 +10566,7 @@ objectives is a planned process. - + drug role @@ -11549,7 +10586,7 @@ objectives is a planned process. - + @@ -11584,7 +10621,7 @@ objectives is a planned process. - + physical document a book is a physical document @@ -11615,24 +10652,16 @@ objectives is a planned process. - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + obsolete processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + PERSON: Alan Ruttenberg + + + obsolete processed material + true @@ -11919,7 +10948,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -11934,7 +10963,7 @@ objectives is a planned process. - + @@ -12041,7 +11070,21 @@ objectives is a planned process. - + + + + + + + + + + + + + + + @@ -12127,7 +11170,7 @@ objectives is a planned process. - + @@ -12190,7 +11233,7 @@ objectives is a planned process. - + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 @@ -12332,38 +11375,21 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - - - - - - - - - - - - - - - - - material processing + + obsolete material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters + PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + OBI branch derived + + + obsolete material processing + true @@ -12478,7 +11504,7 @@ editor = PRS - + @@ -12867,7 +11893,7 @@ specimen can later be subject. - + @@ -13602,7 +12628,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13690,7 +12716,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13986,7 +13012,7 @@ for now. - + @@ -14028,10 +13054,16 @@ for now. + + + + + + plan The plan of researcher X to perform an experiment according to a protocol. - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived @@ -14193,8 +13225,8 @@ for now. - - + + @@ -14273,7 +13305,7 @@ for now. - + @@ -14372,14 +13404,14 @@ for now. - + - + @@ -14442,7 +13474,7 @@ need to add mobile phase as role - + @@ -14515,7 +13547,6 @@ need to add mobile phase as role - @@ -14629,7 +13660,7 @@ Proposal is to obsolete. - + @@ -14791,7 +13822,7 @@ Proposal is to obsolete. - + @@ -15143,7 +14174,7 @@ Proposal is to obsolete. - + @@ -15207,7 +14238,7 @@ Proposal is to obsolete. - + @@ -15468,7 +14499,7 @@ Proposal is to obsolete. - + @@ -15687,7 +14718,7 @@ activity) - + @@ -15708,7 +14739,7 @@ activity) - + @@ -16081,7 +15112,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16243,7 +15274,6 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra @@ -16258,7 +15288,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16327,7 +15357,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16627,7 +15657,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16737,7 +15767,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16747,7 +15777,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + manufacturing @@ -16950,7 +15980,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16963,7 +15993,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. @@ -17152,7 +16182,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -17366,7 +16396,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -17382,7 +16412,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -17689,7 +16719,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -17841,7 +16871,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18201,7 +17231,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18433,7 +17463,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -18802,13 +17832,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -19699,15 +18729,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - @@ -19775,26 +18796,55 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -20229,7 +19279,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20272,11 +19322,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + device setting @@ -20375,7 +19425,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20383,7 +19433,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20850,7 +19900,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + whole organism preparation @@ -21278,7 +20328,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21288,13 +20338,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + animal feeding @@ -21454,7 +20504,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21469,7 +20519,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21741,14 +20791,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -21811,7 +20861,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21879,7 +20929,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21905,7 +20955,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22057,7 +21107,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22081,7 +21131,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22211,7 +21261,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. @@ -22306,7 +21356,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + host role @@ -22526,7 +21576,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. @@ -22580,7 +21630,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22605,7 +21655,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs @@ -22630,13 +21680,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - - - + cloning vector @@ -22783,7 +21831,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site @@ -23255,6 +22302,7 @@ the role 'adjuvant role' inheres in some 'material entity' a + @@ -23489,11 +22537,11 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23565,7 +22613,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23598,7 +22646,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23689,14 +22737,14 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23765,7 +22813,6 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA Amplied DNA created by PCR @@ -23780,7 +22827,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23813,24 +22860,15 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule + true @@ -23884,7 +22922,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution @@ -23921,7 +22959,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -23935,7 +22973,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24193,7 +23231,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24214,7 +23252,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + pill A dose of medicine or placebo in the form of a small pellet. @@ -24273,7 +23311,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24281,7 +23319,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + measurement device A ruler, a microarray scanner, a Geiger counter. @@ -24406,7 +23444,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. @@ -24418,6 +23456,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -24446,7 +23485,7 @@ placeholder - + @@ -24474,7 +23513,7 @@ placeholder - + @@ -24495,7 +23534,7 @@ placeholder - + @@ -24577,23 +23616,14 @@ placeholder - - - - - - - - - - - - - primary structure of RNA molecule + + obsolete primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters - primary structure of RNA molecule + + obsolete primary structure of RNA molecule + true @@ -25144,7 +24174,7 @@ placeholder - + @@ -25467,7 +24497,7 @@ Person: Chris Stoeckert - + @@ -25478,7 +24508,7 @@ Person: Chris Stoeckert - + @@ -25884,7 +24914,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26031,7 +25061,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26055,7 +25085,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - + @@ -26773,8 +25803,8 @@ Updated both textual and logical definition. Both input and output material of f - + labeled specimen A specimen that has been modified in order to be able to detect it in future experiments @@ -26794,7 +25824,7 @@ Updated both textual and logical definition. Both input and output material of f - + infectious agent is a material entity bearing the disposition to infect an organism @@ -26903,7 +25933,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26955,7 +25985,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26963,7 +25993,7 @@ Updated both textual and logical definition. Both input and output material of f - + material separation device flow cytometer @@ -27045,7 +26075,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27122,7 +26152,7 @@ Updated both textual and logical definition. Both input and output material of f - + training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility @@ -27225,7 +26255,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27238,7 +26268,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27351,7 +26381,7 @@ Biochimie. 2010 Feb 18. - + service provider role @@ -27521,14 +26551,14 @@ Biochimie. 2010 Feb 18. - + - + processed specimen @@ -27593,7 +26623,7 @@ Biochimie. 2010 Feb 18. - + @@ -27813,7 +26843,7 @@ Biochimie. 2010 Feb 18. - + @@ -27844,7 +26874,7 @@ Biochimie. 2010 Feb 18. - + @@ -27852,7 +26882,7 @@ Biochimie. 2010 Feb 18. - + container A device that can be used to restrict the location of material entities over time @@ -27866,50 +26896,21 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - device + + obsolete device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - device + + + obsolete device + true @@ -27989,11 +26990,11 @@ In the examples above, a reagent is an operational component of a device, but th - + - + @@ -28004,7 +27005,7 @@ In the examples above, a reagent is an operational component of a device, but th sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data @@ -28111,7 +27112,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28531,7 +27532,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28853,7 +27854,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -28945,7 +27946,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -29332,7 +28333,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -29349,7 +28350,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30083,7 +29084,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30091,7 +29092,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) @@ -30109,7 +29110,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30117,7 +29118,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + perturbation device A homogenizer is a perturbation device. @@ -30137,7 +29138,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30153,7 +29154,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + environmental control device A growth chamber is an environmental control device. @@ -30446,7 +29447,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30532,7 +29533,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30629,7 +29630,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30731,7 +29732,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30751,7 +29752,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30797,7 +29798,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30823,7 +29824,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30883,7 +29884,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31032,7 +30033,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31052,7 +30053,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31283,7 +30284,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31355,7 +30356,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31457,7 +30458,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31477,7 +30478,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31651,7 +30652,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31719,7 +30720,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31864,7 +30865,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31918,7 +30919,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31978,7 +30979,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32046,7 +31047,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32066,7 +31067,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32126,7 +31127,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32365,7 +31366,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32418,7 +31419,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + individual organism identifier @@ -32577,7 +31578,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32676,7 +31677,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. @@ -32819,7 +31820,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -32830,7 +31831,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -33150,7 +32151,7 @@ All subtype will be defined by textual definition now. - + @@ -33166,11 +32167,11 @@ All subtype will be defined by textual definition now. - + - + service @@ -33320,15 +32321,6 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - @@ -33468,13 +32460,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -33486,7 +32478,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms @@ -37726,7 +36718,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -38335,7 +37327,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -40990,32 +39982,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - + genetic characteristics information @@ -43395,7 +42362,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -43424,7 +42391,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44305,7 +43272,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44361,7 +43328,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46020,10 +44987,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + @@ -46044,30 +45011,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + @@ -46727,7 +45684,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + material processing service @@ -47182,7 +46139,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + DNA sequence data @@ -49290,7 +48247,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 @@ -57712,7 +56669,7 @@ is realized in a specimen collection process. - + @@ -58378,7 +57335,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59378,7 +58335,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59730,7 +58687,7 @@ PMID: 23587118. - + @@ -59816,11 +58773,11 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - + - + reagent @@ -60824,7 +59781,7 @@ The following are NOT conclusions based on data: data themselves; results from p - + cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. @@ -61926,7 +60883,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. @@ -62006,7 +60963,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -62142,7 +61099,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay @@ -62298,7 +61255,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -62520,7 +61477,7 @@ PMID: 23587118. - + freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. @@ -62683,7 +61640,7 @@ PMID: 23587118. - + @@ -62718,7 +61675,7 @@ PMID: 23587118. - + @@ -62966,7 +61923,7 @@ PMID: 23587118. - + @@ -63205,7 +62162,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63213,7 +62170,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63276,7 +62233,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63287,7 +62244,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64575,6 +63532,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -64689,6 +63670,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -65665,7 +64670,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -65695,7 +64700,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -67343,11 +66348,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + @@ -70590,7 +69595,7 @@ https://www.doi.org/ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -70705,7 +69710,7 @@ https://www.doi.org/ - + determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. @@ -71707,7 +70712,7 @@ https://www.doi.org/ - + delivery form for hormonal replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. @@ -72310,7 +71315,7 @@ https://www.doi.org/ - + @@ -72321,7 +71326,7 @@ https://www.doi.org/ - + @@ -72884,11 +71889,11 @@ https://www.doi.org/ - + - + @@ -72909,11 +71914,11 @@ https://www.doi.org/ - + - + @@ -73264,7 +72269,7 @@ https://www.doi.org/ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. @@ -76336,7 +75341,7 @@ https://www.doi.org/ - + @@ -76358,7 +75363,7 @@ https://www.doi.org/ - + machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. @@ -78593,7 +77598,7 @@ https://www.doi.org/ 1 - + @@ -78660,7 +77665,7 @@ https://www.doi.org/ - + @@ -78668,7 +77673,7 @@ https://www.doi.org/ - + @@ -78691,7 +77696,7 @@ https://www.doi.org/ - + @@ -78713,7 +77718,7 @@ https://www.doi.org/ - + @@ -81919,7 +80924,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -81927,7 +80932,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + molecular label @@ -82001,7 +81006,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. @@ -82125,7 +81130,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA @@ -82893,7 +81898,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -83079,7 +82084,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -83185,7 +82190,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -83333,7 +82338,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + specimen collection device A device used to collect a specimen. @@ -83402,7 +82407,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -83466,7 +82471,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -83838,7 +82843,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + arthropod trap A device designed to catch arthropods. @@ -83897,7 +82902,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -83957,7 +82962,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + dipper for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. @@ -85421,11 +84426,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -85591,7 +84596,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. @@ -85607,7 +84612,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. @@ -86312,8 +85317,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + @@ -86701,7 +85705,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -86709,7 +85713,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87016,7 +86020,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87037,7 +86041,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. @@ -87414,7 +86418,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + common name of organism @@ -87502,7 +86506,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87513,7 +86517,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -88421,7 +87425,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -90922,7 +89926,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre leukapheresis - A blood harvesting process in which white blood cells are separated from a blood specimen. + A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis @@ -92822,7 +91826,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. @@ -93723,7 +92727,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -93731,7 +92735,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -94652,7 +93656,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf @@ -96267,7 +95271,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -97825,7 +96829,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -98314,7 +97318,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100728,7 +99732,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100736,7 +99740,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100759,7 +99763,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100850,7 +99854,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100858,7 +99862,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100881,7 +99885,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100972,7 +99976,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100980,7 +99984,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -101003,7 +100007,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -102928,14 +101932,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -102948,7 +101952,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasting @@ -102988,7 +101992,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasted @@ -103266,15 +102270,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - @@ -103357,7 +102352,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103791,7 +102785,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103833,7 +102827,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103874,7 +102868,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103942,7 +102936,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103966,7 +102960,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104022,7 +103016,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104033,7 +103027,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104080,7 +103074,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104091,7 +103085,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104138,7 +103132,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104149,7 +103143,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104196,7 +103190,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104207,7 +103201,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104254,7 +103248,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104265,7 +103259,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104312,7 +103306,2360 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + reproductive assay + + A physical examination of an organism that provides information about some reproductive process in that organism. + Jennifer Fostel + reproductive assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + vital sign assay + + An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). + Jennifer Fostel + vital sign assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood pressure assay + + A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. + Jennifer Fostel + blood pressure assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + heart rate variability assay + + A pulse rate assay that measures beat to beat variability in heart beats. + Jennifer Fostel + heart rate variability assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pulse rate assay + + A vital sign assay that measures the heart beat rate of an organism. + Jennifer Fostel + pulse rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + respiratory assay + + A vital sign assay that measures the quality of respiration / respiratory system of an organism + Jennifer Fostel + respiratory assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell differentiation assay + + A cytometry assay that monitors the differentiation stage of cells in culture. + Jennifer Fostel + cell differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell based DNA damage assay + + A cytometry assay that measures DNA damage in cells. + Jennifer Fostel + cell based DNA damage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell count assay + + A cytometry assay to determine the number of natural killer cells in a specimen + Jennifer Fostel + natural killer cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell percentage assay + + A cytometry assay that measures the percentage of natural killer cells in a specimen. + Jennifer Fostel + natural killer cell percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sperm count assay + + A cytometry assay to count the number of mature sperm in a specimen. + Jennifer Fostel + sperm count assay + + + + + + + + + survey administration assay + + An assay that obtains data from one or more participants by using a survey or questionnaire + Jennifer Fostel + survey administration assay + + + + + + + + + maximum data transformation + + A data transformation that has as its output the greatest value in the input data set. + Sebastian Duesing + maximum data transformation + + + + + + + + + minimum data transformation + + A data transformation that has as its output the least value in the input data set. + Sebastian Duesing + minimum data transformation + + + + + + + + + + + + + + + + + + + + + + + + + clinical history collection assay + A clinician asking a patient about the patient's smoking status. + + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. + Sebastian Duesing + HCC + clinical history collection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + disease severity assay + Measuring bone mineral density to determine the severity of osteoporosis. + + An assay that measures the severity of a disease in an organism. + Sebastian Duesing + HCC + disease severity assay + + + + + + + + + + + + + + + genetic characteristic assay + Determining a patient's HLA type. + + An assay that produces information about a genetic characteristic of an organism. + Sebastian Duesing + HCC + genetic characteristic assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood type assay + Identifying a person's ABO blood type. + + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. + Sebastian Duesing + https://medlineplus.gov/ency/article/003345.htm + blood type assay + + + + + + + + + manual muscle testing 8 score + + A clinical data item that quantifies the muscle function of a person based on the person's ability to hold a series of eight body positions that target different muscle groups. + Sebastian Duesing + MMT-8 + https://www.niehs.nih.gov/sites/default/files/research/resources/assets/docs/mmt8_grading_and_testing_procedures_for_the_abbreviated_8_muscle_groups_508.pdf + manual muscle testing 8 score + + + + + + + + + childhood myositis assessment scale score + + A clinical data item that quantifies the degree of muscle function in a child with myositis based on performance of 14 tasks associated with muscular strength and endurance. + Sebastian Duesing + CMAS + https://pubmed.ncbi.nlm.nih.gov/10524696/ + childhood myositis assessment scale score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary electrophoresis mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. + Sebastian Duesing + CE-MS + Thomas Payne + https://en.wikipedia.org/wiki/Capillary_electrophoresis–mass_spectrometry + https://github.com/obi-ontology/obi/issues/1904 + Thomas Payne + capillary electrophoresis mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite outgrowth assay + + A cell differentiation assay that detects neurite outgrowth and/or branching + The UBERON term for neurite is Neuron projection (GO:0043005; A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.). Multiplexed fluorescent imaging can be used to detect nuclei in neuronal cell bodies using Hoechst dye and neurites using anti-beta III-tubulin antibody staining. Commonly measured are neurite length, number and/or number of branch points (arborization). + Jennifer Fostel + neurite outgrowth assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuronal differentiation assay + + A cell differentiation assay that measures differentiation of neurons. + Jennifer Fostel + neuronal differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte differentiation assay + + A cell differentiation assay that measures differentiation of oligodendrocytes. + Jennifer Fostel + oligodendrocyte differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + regulation of synapse maturation assay + + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. + Synaptic puncta is this context is a small (0.5 to 2 um) distinct localized cluster of proteins involved in synaptic transmission. + Jennifer Fostel + regulation of synapse maturation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ames assay + + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. + The bacterial strains were originally constructed by Bruce Ames. Each carries a mutation in a gene involved in histidine synthesis. The cell requires histidine for growth but cannot produce it. The assay measures the creation of mutations that result in a return of function so that the cells can grow on a histidine-free medium. + Jennifer Fostel + Ames assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + micronucleus assay + + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. + The GO term "micronucleus" (GO:0031040) applies to protozoa but does not pertain to this case. Here micronucleus is a chromosome or fragment of a chromosome bounded by nuclear membrane that did not segregate properly at mitosis. + Jennifer Fostel + micronucleus assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PIG-a assay + + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. + The Pig-A gene encodes a product involved in biosynthesis of cell surface anchor glycosylphosphatidylinositol (GPI). + Jennifer Fostel + PIG-a assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin + + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. + Resazurin is the active ingredient in alamar blue; has a blue color and is non-fluorescent. Resorufin has pink color and is fluorescent. Detection of resorufin can be by absorbance or fluorescence. + Jennifer Fostel + Alamar Blue viability assay + cell viability assay based on detection of resorufin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using caspase abundance to detect apoptosis + + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis + Caspases 3 and 7 are frequently used as indicators of apoptosis. + Jennifer Fostel + cell death assay using caspase abundance to detect apoptosis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay + + A cell viability assay which measures the number or proportion of dead cells in a population. + Jennifer Fostel + cell death assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin + Resazurin (active ingredient in alamar blue and CellTiter blue reagents) has a blue color and is not fluorescent. Resorufin is pink and fluorescent. This assay uses the commercial reagent CellTiter Blue (Promega) containing resazurin and fluorescence to detect resorufin. + Jennifer Fostel + CellTiter Blue viability assay + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release + + A cell death assay that measures the release of intracellular LDH. + Jennifer Fostel + cell death assay detecting lactate dehydrogenase (LDH) release + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate + In this assay reagents are added so that LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate, and the NADH converts a tetrazolium salt to a colored formazan product in the presence of an electron acceptor. This formazan product is detected by absorbance quality. + Jennifer Fostel + Cytotox 96 assay + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ovulation assessment in rodent assay + + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. + Jennifer Fostel + Corpus luteum count + ovulation assessment in rodent assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + macroscopic examination of material anatomical entity assay + + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. + Jennifer Fostel + macroscopic examination of material anatomical entity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pathological macroscopic examination of specimen assay + + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. + one objective of this assay is to provide information about the character and extent of changes present and to inform on the cause of death. + Jennifer Fostel + Gross pathology assessment + pathological macroscopic examination of specimen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle assay based on tissue morphology + + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. + Jennifer Fostel + estrous cycle assay based on tissue morphology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo + + An organism development assay performed with a late embryo stage subject. + one objective of this assay is to assess anatomical structures and identify developmental phenotype + Jennifer Fostel + fetal examination + organism development assay in late embryo + + + + + + + + + + + + + + + + + + + + @@ -104323,7 +105670,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104341,24 +105688,26 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - reproductive assay + pregnancy assessment based on tissue morphology assay - A physical examination of an organism that provides information about some reproductive process in that organism. + A histological assay that measures the number of implantation sites in an organism. + An implantation site in this context is the site in the endometrium where the fertilized egg attaches and embeds itself to begin development Jennifer Fostel - reproductive assay + implantation site count + pregnancy assessment based on tissue morphology assay - + - - + + @@ -104370,7 +105719,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104381,7 +105730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104399,24 +105748,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - vital sign assay + cell death assay using vital dye - An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. + Living cells exclude Trypan blue Jennifer Fostel - vital sign assay + cell death assay using vital dye - + - - + + @@ -104428,7 +105778,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104439,7 +105789,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104451,30 +105801,44 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + - + - blood pressure assay + neurite length assay - A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. + A neurite is a neuronal process greater than 10 um extending from a neuron. Jennifer Fostel - blood pressure assay + neurite length assay - + - - + + @@ -104486,7 +105850,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104497,7 +105861,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104511,8 +105875,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + + + + + + + + @@ -104521,24 +105892,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - heart rate variability assay + neurite degree of arborization assay - A pulse rate assay that measures beat to beat variability in heart beats. + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes Jennifer Fostel - heart rate variability assay + neurite branch point count + neurite degree of arborization assay - + - - + + @@ -104550,7 +105922,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104561,7 +105933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104575,8 +105947,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + + + + + + + + @@ -104585,24 +105964,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - pulse rate assay + neurite count assay - A vital sign assay that measures the heart beat rate of an organism. + A cytometry assay that measures the number of neurites in a cultured specimen. + A neurite is a neuronal process greater than 10 um extending from a neuron. Jennifer Fostel - pulse rate assay + neurite count assay - + - - + + @@ -104614,7 +105994,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104625,7 +106005,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104639,34 +106019,30 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - + - - - - + + + + + + - respiratory assay + neuron count assay - A vital sign assay that measures the quality of respiration / respiratory system of an organism + A cytometry assay that measures the number of neurons in a sample Jennifer Fostel - respiratory assay + neuron count assay - + - - + + @@ -104678,7 +106054,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104689,7 +106065,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104701,30 +106077,68 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - cell differentiation assay + cell-body-associated presynaptic puncta count assay - A cytometry assay that monitors the differentiation stage of cells in culture. + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - cell differentiation assay + cell-body-associated presynaptic puncta count assay - + - - + + @@ -104736,7 +106150,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104747,7 +106161,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104767,10 +106181,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -104778,35 +106192,49 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + - + - cell based DNA damage assay + dendrite-associated presynaptic puncta count assay - A cytometry assay that measures DNA damage in cells. + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - cell based DNA damage assay + dendrite-associated presynaptic puncta count assay - + - - + + @@ -104818,7 +106246,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104829,7 +106257,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104841,30 +106269,44 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + - + - natural killer cell count assay + synapse per neuron assay - A cytometry assay to determine the number of natural killer cells in a specimen + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - natural killer cell count assay + synapse per neuron assay - + - - + + @@ -104876,7 +106318,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104887,7 +106329,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104905,24 +106347,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - natural killer cell percentage assay + absorbance quality detection assay - A cytometry assay that measures the percentage of natural killer cells in a specimen. + An assay that measures the absorbance quality of the evaluant + the unit of this assay is absorbance unit (UO:0000269) Jennifer Fostel - natural killer cell percentage assay + absorbance quality detection assay - + - - + + @@ -104931,10 +106374,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -104942,17 +106385,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + @@ -104963,29 +106396,110 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + - sperm count assay + hormone assay - A cytometry assay to count the number of mature sperm in a specimen. + The analyte assay that measures the abundance of a hormone in a specimen. Jennifer Fostel - sperm count assay + hormone assay - + - - - survey administration assay + + + electrocardiograph + + An instrument for recording the changes of electrical potential occurring during the heartbeat used especially in diagnosing abnormalities of heart action. + Jennifer Fostel + https://www.merriam-webster.com/dictionary/electrocardiograph + electrocardiograph + + + + + + + + + biotelemeter - An assay that obtains data from one or more participants by using a survey or questionnaire + A measurement device that also transmits the measurement information from a biological material to a distant station. Jennifer Fostel - survey administration assay + biotelemeter + + + + + + + + + multi-electrode array plate + + A measurement device consisting of grid of tightly spaced microscopic electrodes that can detect the electrical signals of cells in close proximity. + Multielectrode arrays can be embedded in the bottom of a well and cells can be cultured over the electrodes for passive, noninvasive monitoring of electrical activity. + Jennifer Fostel + multi-electrode array plate + + + + + + + + + Transepithelial Electrical Resistance (TEER) device + + A measurement device that measures monolayer barrier integrity via measurement of membrane potential and electrical resistance across a cell monolayer in culture. + Jennifer Fostel + Transepithelial Electrical Resistance (TEER) device + + + + + + + + + randomized clinical trial + + A clinical trial in which the participants are divided by chance into separate groups that compare different treatments or other interventions. Using chance to divide people into groups means that the groups will be similar and that the effects of the treatments they receive can be compared more fairly. At the time of the trial, it is not known which treatment is best. + Sebastian Duesing + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/randomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + randomized clinical trial + + + + + + + + + non-randomized clinical trial + + A clinical trial in which the participants are not assigned by chance to different treatment groups. Participants may choose which group they want to be in, or they may be assigned to the groups by the researchers. + Sebastian Duesing + nonrandomized clinical trial + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/nonrandomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + non-randomized clinical trial @@ -105032,7 +106546,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. @@ -105047,7 +106561,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + chimera An organism which contains cells or tissues with a different genotype @@ -105081,7 +106595,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -105155,31 +106668,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - organism - animal - fungus - plant - virus + + obsolete organism + animal + fungus + plant + virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + WEB: http://en.wikipedia.org/wiki/Organism + + + obsolete organism + true @@ -105340,7 +106844,7 @@ This issue is outside the scope of OBI. - + @@ -105350,7 +106854,7 @@ This issue is outside the scope of OBI. - + xenograft @@ -105369,7 +106873,7 @@ This issue is outside the scope of OBI. - + @@ -105484,7 +106988,7 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- - + screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] @@ -105514,7 +107018,6 @@ change biomaterial to material in definition - synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme @@ -105533,7 +107036,7 @@ DS: Is this synthetic an oxymoron to the biomaterial? - + @@ -105653,7 +107156,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + + + + + + + + + + + + + + + @@ -105685,7 +107202,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -107840,7 +109357,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - + @@ -109697,7 +111214,7 @@ determinations of compounds. - + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. @@ -109784,7 +111301,7 @@ determinations of compounds. - + @@ -109812,7 +111329,7 @@ determinations of compounds. - + @@ -110069,7 +111586,6 @@ determinations of compounds. - denatured polymer Is a polymer which has lost secondary or tertiary structure @@ -110094,7 +111610,7 @@ determinations of compounds. - + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 @@ -110188,7 +111704,6 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 @@ -110207,7 +111722,7 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - + @@ -110215,8 +111730,8 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 + - genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 @@ -110402,7 +111917,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110423,7 +111938,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110456,7 +111971,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110489,11 +112004,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + - + @@ -110538,7 +112053,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110687,7 +112202,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -110753,7 +112268,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110774,7 +112289,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110806,14 +112321,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + - + @@ -110876,7 +112391,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110904,7 +112419,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -110931,7 +112446,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. @@ -111017,7 +112532,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -111235,7 +112750,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112165,7 +113680,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112199,7 +113714,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + particle delivery vessel FC 500 particle delivery vessel @@ -112285,7 +113800,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112307,7 +113822,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112549,7 +114064,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112640,7 +114155,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112711,7 +114226,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112830,7 +114345,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113199,7 +114714,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113374,7 +114889,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113449,7 +114964,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -114107,7 +115622,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114136,14 +115651,14 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114159,7 +115674,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114213,7 +115728,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114230,13 +115745,13 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114316,7 +115831,7 @@ Relates to the creation of a class 'selection rule' - + exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. @@ -114436,7 +115951,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114463,11 +115978,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + @@ -114479,7 +115994,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114675,7 +116190,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114698,7 +116213,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114892,7 +116407,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114914,7 +116429,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114977,7 +116492,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115074,7 +116589,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115096,7 +116611,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115152,7 +116667,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115226,7 +116741,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115266,7 +116781,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115287,17 +116802,17 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + - + @@ -115383,7 +116898,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115779,7 +117294,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115874,7 +117389,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115995,7 +117510,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116110,8 +117625,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + - @@ -116139,7 +117654,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116167,7 +117682,7 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti - + @@ -116235,7 +117750,7 @@ addition of has_role restriction - + @@ -116266,7 +117781,7 @@ old defintion: A mixture (collection) of cell components created by rupturing of - + @@ -116320,7 +117835,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -116350,7 +117864,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. @@ -116675,7 +118189,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + Immunization in vivo @@ -116767,7 +118281,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116883,7 +118397,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116928,7 +118442,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116936,7 +118450,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. @@ -117204,7 +118718,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen @@ -118000,19 +119513,20 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - blood harvesting + blood specimen collection - A material separation where blood is taken from an organism. + A specimen collection in which blood is collected from an organism. IEDB + blood harvesting IEDB - blood harvesting + blood specimen collection @@ -118200,7 +119714,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen @@ -122002,7 +123515,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -147892,18 +149405,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - phenotype - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - - phenotype - - - - @@ -147960,7 +149461,7 @@ realizes some 'host of immune response role' - + treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process @@ -148044,7 +149545,7 @@ realizes some 'host of immune response role' - + parasite organism An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. @@ -148068,7 +149569,7 @@ realizes some 'host of immune response role' - + quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities @@ -148404,7 +149905,7 @@ realizes some 'host of immune response role' - + physical object quality A quality which inheres in a continuant. @@ -148413,6 +149914,30 @@ realizes some 'host of immune response role' + + + + + full-spectrum EM radiation quality + An EM radiation quality that is independent of the EM wavelength range. + + full-spectrum EM radiation quality + + + + + + + + + absorption quality + A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. + + absorption quality + + + + @@ -148918,6 +150443,16 @@ realizes some 'host of immune response role' + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + @@ -149026,12 +150561,40 @@ realizes some 'host of immune response role' + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + protein antithrombin III is a protein + An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein @@ -149279,6 +150842,16 @@ realizes some 'host of immune response role' + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + @@ -149484,6 +151057,18 @@ realizes some 'host of immune response role' + + + + + modified histone + A histone that contains one or more amino acid modifications. + + modified histone + + + + @@ -149519,7 +151104,7 @@ realizes some 'host of immune response role' - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule @@ -149807,6 +151392,18 @@ realizes some 'host of immune response role' + + + + + late embryo + An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. + + late embryo + + + + @@ -149846,7 +151443,18 @@ realizes some 'host of immune response role' + + + + + + + + + + + material anatomical entity Anatomical entity that has mass. @@ -149855,6 +151463,17 @@ realizes some 'host of immune response role' + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + @@ -150095,6 +151714,24 @@ realizes some 'host of immune response role' + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + @@ -150863,6 +152500,18 @@ realizes some 'host of immune response role' + + + + + corpus luteum + A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. + + corpus luteum + + + + @@ -151319,6 +152968,18 @@ realizes some 'host of immune response role' + + + + + phenotype + A phenotypic effect related to http://www.w3.org/2002/07/owl#Thing. + + phenotype + + + + @@ -151336,7 +152997,7 @@ realizes some 'host of immune response role' vaccination - A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. + Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response. vaccination @@ -155642,25 +157303,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - geographic location A reference to a place on the Earth, by its name or by its geographical location. @@ -155678,48 +157320,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -155742,195 +157342,6 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/mirror-ro.owl b/src/ontology/tmp/mirror-ro.owl index a3d3910..fff2d40 100644 --- a/src/ontology/tmp/mirror-ro.owl +++ b/src/ontology/tmp/mirror-ro.owl @@ -9,7 +9,6 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" - xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -17,15 +16,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2025-03-05 + 2025-12-17 https://github.com/oborel/obo-relations/ @@ -42,12 +40,6 @@ - - - - - - @@ -289,17 +281,6 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - @@ -1196,54 +1177,18 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1286,12 +1231,6 @@ Where we have an annotation assertion - - - - - - @@ -1322,30 +1261,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1366,12 +1281,6 @@ Where we have an annotation assertion - - - - - - @@ -1476,30 +1385,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1682,7 +1567,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by @@ -1788,6 +1672,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y + lacks_part + + + + + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) + lacks_plasma_membrane_part + + + + @@ -2356,9 +2258,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure. http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by + innervated by @@ -2736,7 +2643,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + <= Primitive instance level timing relation between events @@ -2753,7 +2660,6 @@ Examples include: the relationship between two channels collected simultaneously x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with @@ -2766,7 +2672,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before @@ -2779,7 +2685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends @@ -2810,7 +2716,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -2827,7 +2733,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by @@ -2840,7 +2746,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts @@ -2857,7 +2763,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts before @@ -2873,7 +2779,6 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland ends_at_start_of meets @@ -2890,7 +2795,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) @@ -2905,7 +2810,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + d during @@ -2923,7 +2828,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + o overlaps @@ -3580,13 +3485,29 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + - + + + + + + + + + + + + + + + + + @@ -3609,6 +3530,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + @@ -3617,6 +3542,18 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. @@ -4271,7 +4208,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of starts with - Chris Mungall Allen starts @@ -4289,7 +4225,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall started by starts with @@ -4361,7 +4296,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ends with - Chris Mungall ends @@ -4377,7 +4311,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall finished by ends with @@ -5017,7 +4950,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -6247,8 +6180,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. @@ -6821,6 +6754,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A relation that holds between a disease or an organism and a phenotype @@ -8257,8 +8191,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -8531,8 +8465,10 @@ the a supports either the existence of b, or the truth value of b. + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI + indicates is marker for @@ -8870,6 +8806,67 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + x is an ectomycorrhizal host of y if and only if x is a plant (Plantae) whose roots form an intercellular interface (aka Hartig net) with fungus (Fungi) y. This interface consists of highly branched hyphae forming a latticework between epidermal and cortical root cells. + + + + An ectomycorrhiza is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. The mycobiont is often from the phyla Basidiomycota and Ascomycota, and more rarely from the Zygomycota. Ectomycorrhizae form on the roots of around 2% of plant species, usually woody plants, including species from the birch, dipterocarp, myrtle, beech, willow, pine and rose families. Research on ectomycorrhizae is increasingly important in areas such as ecosystem management and restoration, forestry, and agriculture. Unlike other mycorrhizal relationships, such as arbuscular mycorrhiza and ericoid mycorrhiza, ectomycorrhizal fungi do not penetrate their host's cell wall. Instead they form an entirely intercellular interfaces known as the Hartig net, consisting of highly branched hyphae forming a latticework between epidermal and cortical root cells. + ectomycorrhizal host of + + + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + inverse of ectomycorrhizal host of + + has ectomycorrhizal host + + + + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + x is an arbuscular mycorrhizal host of y if and only if x is a vascular plant (Plantae) whose cortical cells of the roots are penetrated by fungus (Fungi) y and form arbuscules. + + + + An arbuscular mycorrhiza (AM) (plural mycorrhizae) is a type of mycorrhiza in which the symbiont fungus (Arbuscular mycorrhizal fungi, or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza (not to be confused with ectomycorrhiza). They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered. Arbuscular mycorrhizae are formed by fungi in the subphylum Glomeromycotina and some fungi from the Mucoromycotina. These subphyla, along with the Mortierellomycotina, form the phylum Mucoromycota, a sister clade of the more well-known and diverse dikaryan fungi. AM fungi help plants to capture nutrients such as phosphorus, sulfur, nitrogen and micronutrients from the soil. It is believed that the development of the arbuscular mycorrhizal symbiosis played a crucial role in the initial colonisation of land by plants and in the evolution of the vascular plants. It has been said that it is quicker to list the plants that do not form endomycorrhizae than those that do. This symbiosis is a highly evolved mutualistic relationship found between fungi and plants, the most prevalent plant symbiosis known, and AMF is found in 80% of vascular plant families in existence today. + arbuscular mycorrhizal host of + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + inverse of arbuscular mycorrhizal host of + + + has arbuscular mycorrhizal host + + + + @@ -9762,8 +9759,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9775,8 +9772,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9808,7 +9805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. @@ -9899,7 +9896,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -10855,6 +10852,24 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + The information in a blueprint specifies the dimensions of a building. + The information in a recipe specifies what interredients to use and the steps needed to prepare a meal. + The information in a software program specifies the order of computations. + A relation between information and an entity such that the information serves as a rule or guide if the entity is an occurrent, or the information serves as a model if the entity is a continuant. + + 2025-06-16T17:08:04Z + prescribes + specifies + information specifies + https://www.ontologyrepository.com/CommonCoreOntologies/prescribes + + + + @@ -10910,6 +10925,17 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + inverse of 'has symptom' + + 2025-06-16T17:42:05Z + symptom of + + + + @@ -10942,6 +10968,29 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + Inverse of information specifies. + + 2025-06-16T17:13:17Z + specified by information + + + + + + + + + Inverse relation of 'is marker for'. + + 2025-07-14T20:57:25Z + has marker + + + + @@ -11316,6 +11365,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context. + Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals. + + + has substitutable entity + + + + @@ -11437,86 +11499,321 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - This relation groups relations between diseases and any other kind of entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - - 2018-09-26T00:00:32Z - disease relationship + + + A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + provides clinical information for - + - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - - 2018-09-26T01:08:58Z - results in changes to anatomical or cellular structure + + + A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue. + An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype. + https://orcid.org/0000-0001-5809-9523 + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + diagnostic for - + - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - TODO: Add homeomorphy axiom - - - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - + + + Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression. + A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The status of 'd' refers to disease progression/remission or treatment response. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors status of - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - + - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - + + + The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates response to - - - - Similarity that results from common evolutionary origin. - - + + + + + + + + The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug. + +Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + predicts effect of + + + + + + + + + A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + prognostic for + + + + + + + + + As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + assesses toxicity of + + + + + + + + + The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates risk of developing + + + + + + + + + An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy. + A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates clinical effect of + + + + + + + + + The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors effect of + + + + + + + + + The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers: + - 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest; + - 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent; + - 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent. + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors exposure to + + + + + + + + + A polyubiquitin has_constituent_monomer some ubiquitin. + An amino acid chain has_constituent_monomer at least two amino acid residues. + A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer 'm' if and only if P has_component multiple instances of 'm' and each instance of 'm' is covalently attached to another instance of 'm'. + + Usage note: The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows the number of instances of 'm' to be indicated. + has constituent monomer + + + + + + + + + + Charged tRNA (i.e., aminoacyl-tRNA) is a tRNA that is covalently_bound_to some amino acid. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of covalent interactions. + + Such entities will colocalize at all times of the interaction. + covalently bound to + + + + + + + + + + Holo-calmodulin is a calmodulin that is non-covalently_bound_to calcium. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions. + + Such entities will colocalize at all times of the interaction. + non-covalently bound to + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + @@ -11529,7 +11826,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - + homoplasous to analogy @@ -11553,7 +11850,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - + ECO:0000075 homocracous to @@ -11579,7 +11876,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - + analogy Convergence usually implies a notion of adaptation. @@ -11602,7 +11899,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. @@ -11625,7 +11922,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - + ECO:0000071 MI:2163 @@ -11652,7 +11949,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - + homology ECO:0000080 @@ -11687,7 +11984,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - + ECO:0000067 biological homologous to @@ -11713,7 +12010,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - + atavism rudiment @@ -11737,7 +12034,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - + MeSH:Synteny SO:0000860 @@ -11764,7 +12061,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - + SO:0000854 SO:0000859 @@ -11792,7 +12089,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - + syntenic paralogous to duplicon @@ -11817,7 +12114,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - + syntenic orthologous to in syntenic orthology relationship with @@ -11839,7 +12136,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - + fractional homology partial homologous to @@ -11868,7 +12165,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - + MeSH:Structural_Homology,_Protein protein structural homologous to @@ -11892,7 +12189,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - + pseudogene SO:non_functional_homolog_of @@ -11916,7 +12213,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - + ECO:00000060 SO:0000855 @@ -11946,7 +12243,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). @@ -11970,7 +12267,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - + 1 to 1 homologous to 1:1 homology @@ -11995,7 +12292,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - + 1 to 1 orthologous to 1:1 orthology @@ -12020,7 +12317,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - + ohnologous to homoeology @@ -12044,7 +12341,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - + in-paralogous to inparalogy @@ -12068,7 +12365,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - + alloparalogy out-paralogous to @@ -12092,7 +12389,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - + pro-orthologous to in pro-orthology relationship with @@ -12115,7 +12412,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - + semi-orthologous to The converse of pro-orthologous. @@ -12139,7 +12436,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - + serial homologous to homonomy @@ -12162,7 +12459,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - + heterochronous homologous to heterochrony @@ -12186,7 +12483,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - + juvenification pedomorphosis @@ -12210,7 +12507,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - + in peramorphosis relationship with @@ -12231,7 +12528,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - + in progenesis relationship with @@ -12253,7 +12550,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - + juvenilization neotenous to @@ -12277,7 +12574,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - + mimicrous to in mimicry relationship with @@ -12300,7 +12597,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - + 1 to many orthologous to 1:many orthology @@ -12327,7 +12624,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - + many to many homologous to many-to-many homology @@ -12351,7 +12648,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - + 1 to many homologous to one-to-many homology @@ -12376,7 +12673,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - + apomorphous to synapomorphy @@ -12399,7 +12696,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - + plesiomorphous to symplesiomorphy @@ -12424,7 +12721,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - + deep genetic homology deep homologous to @@ -12451,7 +12748,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - + hemiplasous to in hemiplasy relationship with @@ -12473,7 +12770,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - + gametologous to in gametology relationship with @@ -12495,7 +12792,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - + MeSH:Chromosome_Pairing chromosomal homologous to @@ -12519,7 +12816,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - + many to many orthologous to many-to-many orthology @@ -12548,7 +12845,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - + within-species paralogous to in within-species paralogy relationship with @@ -12570,7 +12867,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - + between-species paralogous to The genes have diverged before a speciation event. @@ -12593,7 +12890,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - + post-displacement in postdisplacement relationship with @@ -12615,7 +12912,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - + in hypermorphosis relationship with @@ -12637,7 +12934,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - + synologous to in synology relationship with @@ -12661,7 +12958,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - + ECO:0000080 isoorthologous to @@ -12684,7 +12981,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - + tandem paralogous to iterative paralogy @@ -12710,7 +13007,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - + apomorphic tendency cryptic homology @@ -12742,7 +13039,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - + generative homology syngenous to @@ -12768,7 +13065,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - + 1:1 paralogy apparent 1:1 orthology @@ -12795,7 +13092,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. @@ -12819,7 +13116,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - + equivalogous to This may include examples of orthology, paralogy and xenology. @@ -12842,7 +13139,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - + interologous to in interology relationship with @@ -12865,7 +13162,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - + functional similarity in functional equivalence relationship with @@ -12888,7 +13185,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - + iterative homologous to in iterative homology relationship with @@ -12910,7 +13207,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - + duplicate xenology multiple xenology @@ -12934,7 +13231,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - + plerologous to This phenomenon is usually due to gene conversion process. @@ -12958,7 +13255,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. @@ -12983,7 +13280,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - + heterotopy in homeosis relationship with @@ -13007,7 +13304,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. @@ -13031,7 +13328,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - + axis paramorphism in paramorphism relationship with @@ -13054,7 +13351,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - + regulogous to in regulogy relationship with @@ -13446,6 +13743,38 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + completely executed planned process + + + + @@ -13462,6 +13791,16 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A processed material entity which is designed to be capable of a process. + device + + + + @@ -13487,14 +13826,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu An environmental system which can sustain and allow the growth of an ecological population. - - EcoLexicon:habitat LTER:238 SWEETRealm:Habitat - A habitat's specificity to an ecological population differentiates it from other environment classes. See Buttigieg et al. (2016; https://doi.org/10.1186/s13326-016-0097-6) for an explanation of ENVO's treatement of habitats. 3,849 of such habitat classes are available here: https://github.com/EnvironmentOntology/envo-habitats + https://en.wikipedia.org/wiki/Habitat + A habitat's specificity to an ecological population differentiates it from other environment classes. habitat + + + + An environmental system which can sustain and allow the growth of an ecological population. + EnvO:EnvO + @@ -13600,7 +13944,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3781009 Reactome:R-HSA-3788724 Reactome:R-HSA-3797226 - Reactome:R-HSA-400267 Reactome:R-HSA-4332236 Reactome:R-HSA-446877 Reactome:R-HSA-450358 @@ -13649,6 +13992,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-975118 Reactome:R-HSA-975147 Reactome:R-HSA-9758604 + Reactome:R-HSA-9766227 Reactome:R-HSA-9793444 Reactome:R-HSA-9793485 Reactome:R-HSA-9793679 @@ -13665,6 +14009,10 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9834070 Reactome:R-HSA-9861563 Reactome:R-HSA-9861640 + Reactome:R-HSA-9929350 + Reactome:R-HSA-9934753 + Reactome:R-HSA-9948301 + Reactome:R-HSA-9954721 ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity @@ -14083,12 +14431,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3797226 Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) - - - - Reactome:R-HSA-400267 - BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins - @@ -14249,7 +14591,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-69598 - Ubiquitination of phosphorylated Cdc25A + Ubiquitination of phosphorylated CDC25A @@ -14377,6 +14719,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9758604 Ubiquitination of IKBKG by TRAF6 + + + + Reactome:R-HSA-9766227 + MDM2 mediates CDH1 ubiquitination + @@ -14473,6 +14821,30 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9861640 CTLH E3 ligase ubiquitinates PKM-1 + + + + Reactome:R-HSA-9929350 + Ubiquitination of CD274 by BTRC-SCF E3-ligase complex + + + + + Reactome:R-HSA-9934753 + CBLL1 ubiquitinates CDH1 + + + + + Reactome:R-HSA-9948301 + ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit + + + + + Reactome:R-HSA-9954721 + NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide + @@ -14509,7 +14881,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z @@ -14638,44 +15009,22 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process - + - + - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - + - + assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. @@ -14694,7 +15043,6 @@ objectives is a planned process. - container A device that can be used to restrict the location of material entities over time @@ -14705,56 +15053,6 @@ objectives is a planned process. - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - @@ -14950,6 +15248,7 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 + FAO:0000001 FMA:305751 FMA:67135 GAID:781 @@ -14967,6 +15266,7 @@ This issue is outside the scope of OBI. connected biological structure UBERON:0000061 + @@ -15335,73 +15635,596 @@ This issue is outside the scope of OBI. - + - - example to be eventually removed - example to be eventually removed + + + + 2019-03-05T17:25:21Z + Western Australia Ecoregion + WWF:AA1310 + https://www.worldwildlife.org/ecoregions/aa1310 + Western Australian Mulga Shrublands Ecoregion - + - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete + + + 2019-03-05T17:51:32Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Australasia Ecoregion - + - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term + + + + 2019-03-05T17:52:41Z + Southern central Australia Ecoregion + WWF:AA1309 + https://www.worldwildlife.org/ecoregions/aa1309 + Tirari-Sturt Stony Desert Ecoregion - + - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release + + + + 2019-03-05T17:54:35Z + Eastern central Australia Ecoregion + WWF:AA1308 + https://www.worldwildlife.org/ecoregions/aa1308 + Simpson Desert Region - + - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete + + + + 2019-03-05T17:56:13Z + Western Australia Ecoregion + WWF:AA1307 + https://www.worldwildlife.org/ecoregions/aa1307 + Pilbara Shrublands Ecoregion - + - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated + + + + 2019-03-05T18:10:52Z + Western coast of Australia Ecoregion + WWF:AA1301 + https://www.worldwildlife.org/ecoregions/aa1301 + Carnarvon Xeric Shrublands Ecoregion - + - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + + + + 2019-03-05T18:12:28Z + Central Australia Ecoregion + WWF:AA1302 + https://www.worldwildlife.org/ecoregions/aa1302 + Central Ranges Xeric Shrub Ecoregion + + + + + + + + + + 2019-03-05T18:15:11Z + Western central Australia + WWF:AA1303 + https://www.worldwildlife.org/ecoregions/aa1303 + Gibson Desert Ecoregion + + + + + + + + + + 2019-03-05T18:17:15Z + Northwestern Australia + WWF:AA1304 + https://www.worldwildlife.org/ecoregions/aa1304 + The Great Sandy-Tanami Desert Ecoregion + + + + + + + + + + 2019-03-05T18:24:06Z + Southern Australia Ecoregion + WWF:AA1305 + https://www.worldwildlife.org/ecoregions/aa1305 + Great Victoria Desert Ecoregion + + + + + + + + + + 2019-03-05T18:26:16Z + Southern Australia Ecoregion + WWF:AA1306 + https://www.worldwildlife.org/ecoregions/aa1306 + Nullarbor Plains Xeric Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:01:41Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Afrotropical Ecoregion + + + + + + + + + + 2019-03-06T22:02:37Z + Southern Africa: Southern Namibia into South Africa + WWF:AT1322 + https://www.worldwildlife.org/ecoregions/at1322 + Succulent Karoo Ecoregion + + + + + + + + + + 2019-03-06T22:07:38Z + WWF:AT1321 + https://www.worldwildlife.org/ecoregions/at1321 + Arabian Peninsula: Yemen and Saudi Arabia + Yemen and Saudi Arabia Ecoregion + + + + + + + + + + 2019-03-06T22:11:38Z + WWF:AT1320 + https://www.worldwildlife.org/ecoregions/at1320 + Arabian Peninsula: Yemen, Saudi Arabia, and Oman + Yemen, Saudi Arabia, and Oman Ecoregion + + + + + + + + + + 2019-03-06T22:13:00Z + WWF:AT1319 + https://www.worldwildlife.org/ecoregions/at1319 + Somali montane xeric woodlands ecoregion + Somali Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-06T22:15:07Z + Islands east of the Horn of Africa and south of Yemen Ecoregion + WWF:AT1318 + https://www.worldwildlife.org/ecoregions/at1318 + Socotran Archipelago Ecoregion + + + + + + + + + 2019-03-06T22:18:55Z + WWF:AT1317 + https://www.worldwildlife.org/ecoregions/at1317 + Red Sea Coastal Desert Ecoregion + + + + + + + + + 2019-03-06T22:20:56Z + WWF:AT1316 + https://www.worldwildlife.org/ecoregions/at1316 + Namibian Savanna Woodland Ecoregion + + + + + + + + + 2019-03-06T22:24:28Z + Africa: Namibia Ecoregion + WWF:AT1315 + https://www.worldwildlife.org/ecoregions/at1315 + Namib Desert Ecoregion + + + + + + + + + 2019-03-06T22:26:15Z + WWF:AT1314 + https://www.worldwildlife.org/ecoregions/at1314 + Nama Karoo Ecoregion + + + + + + + + + 2019-03-06T22:28:43Z + WWF:AT1313 + https://www.worldwildlife.org/ecoregions/at1313 + Masai Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-06T22:30:23Z + WWF:AT1312 + https://www.worldwildlife.org/ecoregions/at1312 + Madagascar Succulent Woodlands Ecoregion + + + + + + + + + 2019-03-06T22:31:29Z + WWF:AT1311 + https://www.worldwildlife.org/ecoregions/at1311 + Madagascar spiny desert ecoregion + Madagascar Spiny Thickets Ecoregion + + + + + + + + + 2019-03-06T22:39:32Z + WWF:AT1310 + https://www.worldwildlife.org/ecoregions/at1310 + Africa: Coastal Namibia and Angola Ecoregion + Kaokoveld Desert Ecoregion + + + + + + + + + 2019-03-06T22:42:47Z + WWF:AT1309 + https://www.worldwildlife.org/ecoregions/at1309 + Kalahari Xeric Savanna Ecoregion + + + + + + + + + 2019-03-06T22:44:54Z + WWF:AT1308 + https://www.worldwildlife.org/ecoregions/at1308 + Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion + Ile Europa and Bassas da India Ecoregion + + + + + + + + + 2019-03-06T22:46:58Z + Eastern Africa: Somalia + WWF:AT1307 + https://www.worldwildlife.org/ecoregions/at1307 + Hobyo Grassland and Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:54:57Z + WWF:AT1306 + https://www.worldwildlife.org/ecoregions/at1306 + Arabian Peninsula: Oman and United Arab Emirates Ecoregion + Oman and United Arab Emirates Ecoregion + + + + + + + + + 2019-03-07T00:08:06Z + WWF:AT1305 + https://www.worldwildlife.org/ecoregions/at1305 + Ethiopian Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-07T00:11:29Z + WWF:AT1304 + https://www.worldwildlife.org/ecoregions/at1304 + Eritrean Coastal Desert Ecoregion + + + + + + + + + 2019-03-07T00:13:33Z + WWF:AT1303 + https://www.worldwildlife.org/ecoregions/at1303 + North central Africa: Eastern Chad and small area of western Sudan + East Saharan Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-07T00:16:12Z + WWF:AT1302 + https://www.worldwildlife.org/ecoregions/at1302 + Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion + Oman, Yemen, and Saudi Arabia Ecoregion + + + + + + + + + 2019-03-07T00:18:09Z + WWF:AT1301 + https://www.worldwildlife.org/ecoregions/at1301 + Aldabra Island Xeric Scrub Ecoregion + + + + + + + + 2019-04-26T23:38:50Z + + Indo-Malay Ecoregion + + + + + + + + + 2019-04-26T23:40:13Z + + WWF:IM1304 + Southern Asia: Western India into Pakistan + Thar Desert + + + + + + + + + 2019-04-27T00:12:51Z + + WWF:IM1303 + Southern Asia: Eastern India and western Pakistan + Northwestern Thorn Scrub Forests + + + + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + envoAtmo + envoPolar + Arctic front + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + + + + + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + envoAtmo + envoPolar + Antarctic front + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + + + + + + + + + + Stellar radiation emitted from Sol. + Solar radiation + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -15493,6 +16316,69 @@ binary, and takes no temporal argument. + + + + researcher + Nicole Vasilevsky + + + + + researcher + + + + + + Nicole Vasilevsky + + + + + + + + + researcher + Darren A. Natale + + + + + researcher + + + + + + Darren A. Natale + + + + + + + + + researcher ORCID ID = 0000-0001-5948-3092 + Marta Costa + + + + + researcher ORCID ID = 0000-0001-5948-3092 + + + + + + Marta Costa + + + + + @@ -15535,6 +16421,27 @@ binary, and takes no temporal argument. + + + + researcher + Katja S Schulz + + + + + researcher + + + + + + Katja S Schulz + + + + + @@ -15556,6 +16463,27 @@ binary, and takes no temporal argument. + + + + researcher + David P Hill + + + + + researcher + + + + + + David P Hill + + + + + @@ -15598,6 +16526,48 @@ binary, and takes no temporal argument. + + + + American epidemiologist and ontologist + Melissa Haendel + + + + + American epidemiologist and ontologist + + + + + + Melissa Haendel + + + + + + + + + researcher + Jennifer Deegan + + + + + researcher + + + + + + Jennifer Deegan + + + + + @@ -15619,6 +16589,48 @@ binary, and takes no temporal argument. + + + + researcher + Alexander D Diehl + + + + + researcher + + + + + + Alexander D Diehl + + + + + + + + + researcher + Matthew Brush + + + + + researcher + + + + + + Matthew Brush + + + + + @@ -15682,6 +16694,48 @@ binary, and takes no temporal argument. + + + + researcher + Tanya Z Berardini + + + + + researcher + + + + + + Tanya Z Berardini + + + + + + + + + researcher + Sabrina Toro + + + + + researcher + + + + + + Sabrina Toro + + + + + @@ -15703,6 +16757,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0002-5260-9315 + Patrick Ray + + + + + Researcher ORCID=0000-0002-5260-9315 + + + + + + Patrick Ray + + + + + @@ -15955,6 +17030,27 @@ binary, and takes no temporal argument. + + + + researcher + Terrence F Meehan + + + + + researcher + + + + + + Terrence F Meehan + + + + + @@ -16015,6 +17111,33 @@ binary, and takes no temporal argument. Charles Tapley Hoyt + + + + + + + researcher + Vasundra Touré + + + + + researcher + + + + + + Vasundra Touré + + + + + + + + @@ -16045,7 +17168,8 @@ binary, and takes no temporal argument. failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg failed exploratory term @@ -16073,21 +17197,26 @@ binary, and takes no temporal argument. placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. placeholder removed terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. term imported term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. term split @@ -16216,6 +17345,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Add as annotation triples in the granting ontology is allocated id range + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. @@ -16378,7 +17513,7 @@ No imports The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. out of scope @@ -16394,66 +17529,84 @@ No imports domain entity does not exist + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + 2025-06-02 + preferred label for community + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms + 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms + 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms + 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms + 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms + 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants + 2023-03-03 UK spelling synonym A synonym type for common misspellings + 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. + 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name + 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + 2023-09-30 INN International Nonproprietary Name @@ -16461,18 +17614,21 @@ No imports nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. + 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + 2023-11-01 acronym A serial number such as "12324X"; a stop sign; a written proper name such as "OBI An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 2024-03-25 has symbol @@ -16597,15 +17753,15 @@ No imports - - - + + + @@ -16616,6 +17772,7 @@ No imports + if effector directly negatively regulates X, its parent MF directly negatively regulates X @@ -16623,9 +17780,9 @@ No imports - - - + + + @@ -16634,9 +17791,9 @@ No imports - - - + + + @@ -16650,9 +17807,9 @@ No imports - - - + + + @@ -16660,6 +17817,7 @@ No imports + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16667,9 +17825,9 @@ No imports - - - + + + @@ -16678,9 +17836,9 @@ No imports - - - + + + @@ -16693,17 +17851,29 @@ No imports - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16711,9 +17881,9 @@ No imports - - - + + + @@ -16721,24 +17891,13 @@ No imports - - - + + + + - - - - - - - - - - - - - + @@ -16748,13 +17907,24 @@ No imports - - - - + + + - + + + + + + + + + + + + + @@ -16766,9 +17936,9 @@ No imports - - - + + + @@ -16776,9 +17946,10 @@ No imports - - - + + + + @@ -16792,9 +17963,9 @@ No imports - - - + + + @@ -16809,9 +17980,9 @@ No imports - - - + + + @@ -16819,9 +17990,10 @@ No imports - - - + + + + @@ -16835,9 +18007,9 @@ No imports - - - + + + @@ -16852,9 +18024,9 @@ No imports - - - + + + @@ -16862,9 +18034,10 @@ No imports - - - + + + + @@ -16878,9 +18051,9 @@ No imports - - - + + + @@ -16895,9 +18068,9 @@ No imports - - - + + + @@ -16905,9 +18078,10 @@ No imports - - - + + + + @@ -16921,9 +18095,9 @@ No imports - - - + + + @@ -16931,9 +18105,6 @@ No imports - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg @@ -16941,9 +18112,9 @@ No imports - - - + + + @@ -16952,36 +18123,12 @@ No imports - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -16992,9 +18139,9 @@ No imports - - - + + + @@ -17002,18 +18149,16 @@ No imports - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -17022,25 +18167,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -17051,9 +18183,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17061,9 +18193,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP @@ -17071,8 +18200,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17081,9 +18210,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17091,10 +18220,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -17110,9 +18238,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17127,9 +18255,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17138,37 +18266,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -17179,9 +18281,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17189,8 +18291,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction @@ -17198,9 +18298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17208,26 +18308,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17238,9 +18324,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17248,7 +18334,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg reg edge from input to regulatory subfunction @@ -17256,9 +18341,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17266,26 +18351,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17296,9 +18367,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17306,7 +18377,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct positive reg edge from input to regulatory subfunction @@ -17314,9 +18384,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17324,26 +18394,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17354,9 +18410,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17364,7 +18420,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - effector input is compound function input + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg @@ -17372,9 +18430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17383,12 +18441,36 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17400,8 +18482,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17409,17 +18491,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - Input of effector is input of its parent MF + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts - - - - + + + @@ -17428,12 +18511,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17444,9 +18540,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17454,17 +18550,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly regulates X, its parent MF directly regulates X + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP - - - - + + + @@ -17473,12 +18570,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17487,11 +18597,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - + + + + + @@ -17499,7 +18609,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17507,9 +18616,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17517,13 +18626,38 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17534,9 +18668,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17544,7 +18678,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly negatively regulates X, its parent MF directly negatively regulates X + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction @@ -17552,9 +18687,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17563,12 +18698,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17579,9 +18727,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17589,7 +18737,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct neg reg edge from input to regulatory subfunction @@ -17597,9 +18745,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17608,12 +18756,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17623,29 +18784,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct positive reg edge from input to regulatory subfunction @@ -17653,9 +18803,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17664,12 +18814,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17679,28 +18842,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + + effector input is compound function input @@ -17708,9 +18861,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17719,9 +18872,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17735,9 +18888,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17745,6 +18898,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + Input of effector is input of its parent MF @@ -17752,9 +18906,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17763,9 +18917,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17779,9 +18933,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17789,6 +18943,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly regulates X, its parent MF directly regulates X @@ -17796,9 +18951,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17807,9 +18962,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17823,9 +18978,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17833,6 +18988,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17840,9 +18996,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17851,9 +19007,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17867,9 +19023,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/src/ontology/tmp/obi-download.owl b/src/ontology/tmp/obi-download.owl index e6bda0f..5f39d3b 100644 --- a/src/ontology/tmp/obi-download.owl +++ b/src/ontology/tmp/obi-download.owl @@ -7,15 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -82,7 +79,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2025-05-01 + 2025-12-18 @@ -104,29 +101,6 @@ - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - @@ -138,7 +112,6 @@ The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred label editor preferred term editor preferred term @@ -155,7 +128,6 @@ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage @@ -216,7 +188,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition definition textual definition @@ -232,7 +203,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note @@ -247,7 +217,6 @@ We also have the outstanding issue of how to aim different definitions to differ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor @@ -263,9 +232,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - alternative term @@ -279,7 +246,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source @@ -304,7 +270,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note @@ -360,7 +325,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from @@ -509,7 +473,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation @@ -522,7 +485,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language - has associated axiom(nl) @@ -535,7 +497,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) @@ -600,7 +561,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label @@ -912,12 +872,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1051,12 +1005,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1185,6 +1133,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -1194,12 +1148,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1295,12 +1243,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1316,12 +1258,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1414,18 +1336,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - has part @@ -1434,18 +1346,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + realized in @@ -1456,13 +1358,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1471,15 +1367,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + preceded by @@ -1488,50 +1379,43 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + precedes - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + executed by + + + + + + + + intended to realize - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + has plan + + + + + + + + intended plan process type @@ -1551,6 +1435,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is about A (currently) primitive relation that relates an information artifact to an entity. @@ -1654,11 +1539,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has specified input see is_input_of example_of_usage - The inverse property of is specified input of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters @@ -1690,11 +1575,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of @@ -1743,10 +1628,10 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - + has specified output - The inverse property of is specified output of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter @@ -1910,10 +1795,10 @@ instance level relation [GOC:cjm] - + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of @@ -2011,7 +1896,7 @@ level of radioactivity is_proxy_for level of toxicity - + achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' @@ -2130,7 +2015,7 @@ level of radioactivity is_proxy_for level of toxicity - + objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. @@ -2255,15 +2140,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + - @@ -2377,15 +2262,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2394,16 +2271,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - has characteristic @@ -2412,15 +2280,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -2429,16 +2289,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2447,11 +2298,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as @@ -2461,10 +2307,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes @@ -2474,15 +2316,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this catalysis function is a function of this enzyme + function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of @@ -2491,14 +2327,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this red color is a quality of this apple + quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of @@ -2507,14 +2338,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this investigator role is a role of this person + role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of @@ -2523,13 +2349,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + has function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function + has function @@ -2538,12 +2360,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this apple has quality this red color + has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality + has quality @@ -2552,13 +2371,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) + has role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role + has role @@ -2567,11 +2382,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - + has disposition a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition @@ -2580,8 +2393,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + inverse of has disposition + disposition of @@ -2590,47 +2404,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - derives from - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - + derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from derives from - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -2640,97 +2425,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in + located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by @@ -2739,11 +2446,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes @@ -2752,14 +2456,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - + has component - @@ -2767,11 +2467,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - has function realized in - capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of @@ -2779,9 +2480,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - surrounded by - x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by @@ -2796,15 +2496,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + inverse of surrounded by + surrounds + + + + - - - move to BFO? - Allen - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation + temporally related to + + temporally related to @@ -2812,61 +2518,50 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + starts inverse of starts with - Chris Mungall - Allen + starts - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + has output - + - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true + + inverse of enables + enabled by - + - - DEPRECATED bearer of - true + + + has member + has member is a mereological relation between a collection and an item. + + has member @@ -2888,6 +2583,41 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + has quantity + + + + + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + @@ -2972,518 +2702,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - @@ -3491,226 +2715,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - @@ -3718,183 +2733,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - @@ -3902,105 +2742,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - site - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -4008,439 +2751,40 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - material - MaterialEntity + material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - + immaterial entity - + - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - @@ -4449,7 +2793,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ insulin - A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the β cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. insulin @@ -4459,7 +2803,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -4471,7 +2815,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -4491,7 +2835,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + An organic heterobicyclic compound that consists of 2-oxohexahydro-1<em>H</em>-thieno[3,4-<em>d</em>]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin @@ -4501,9 +2845,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3β-hydroxy group. cholesterol @@ -4513,7 +2857,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -4525,7 +2869,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -4537,7 +2881,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -4549,9 +2893,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + A one-carbon compound with formula CO<small><sub>2</sub></small> in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide @@ -4563,7 +2907,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide @@ -4573,7 +2917,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -4585,7 +2929,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -4597,9 +2941,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + A member of the class of 2-benzofurans that is 2-benzofuran-1(3<em>H</em>)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2<i>E</i>)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by <em>Penicillium brevi-compactum, P. stoloniferum, P. echinulatum</em> and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. mycophenolic acid @@ -4609,7 +2953,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -4621,7 +2965,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -4645,9 +2989,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + progesterone - A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + A C<small><sub>21</sub></small>-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. progesterone @@ -4657,7 +3001,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogensulfite hydrogensulfite @@ -4668,7 +3012,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -4680,7 +3024,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -4692,9 +3036,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + testosterone - An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + An androstanoid having 17β-hydroxy and 3-oxo groups, together with unsaturation at C-4‒C-5.. testosterone @@ -4704,9 +3048,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + A hemoprotein that is the ferric (Fe<small><sup>3+</small></sup>) form of hemoglobin. methemoglobin @@ -4716,7 +3060,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -4728,9 +3072,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. + A 17α-hydroxy-C<small><sub>21</sub></small>-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -4740,7 +3084,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -4752,7 +3096,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -4764,7 +3108,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -4776,7 +3120,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -4788,7 +3132,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -4797,23 +3141,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - molecular entity - - - - - + cytochalasin cytochalasin @@ -4824,7 +3155,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -4836,21 +3167,35 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + A member of the class of <em>N</em>-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea + + + + + hormone + Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. + + hormone + + + + - + + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton @@ -4860,7 +3205,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + iron cation iron cation @@ -4871,7 +3216,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -4883,7 +3228,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -4895,7 +3240,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -4907,7 +3252,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -4919,7 +3264,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lead(0) lead(0) @@ -4930,9 +3275,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + A complex glycopeptide from <em>Streptomyces orientalis</em>. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria <em>Staphylococcus aureus</em> and <em>Clostridium difficile</em>. vancomycin @@ -4944,7 +3289,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + A racemate comprising equimolar amounts of (<i>R</i>)- and (<i>S</i>)-lactic acid. rac-lactic acid @@ -4954,7 +3299,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -4966,9 +3311,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + An androstanoid that is androst-5-ene substituted by a β-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. dehydroepiandrosterone @@ -4978,7 +3323,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -4989,7 +3334,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -5001,7 +3346,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -5013,7 +3358,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -5025,7 +3370,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydroxyl hydroxyl @@ -5036,20 +3381,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek δευτερον, second). deuterium atom + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -5061,7 +3415,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ruthenium atom ruthenium atom @@ -5090,7 +3444,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -5102,7 +3456,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5114,9 +3468,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red @@ -5126,7 +3480,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -5138,7 +3492,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methyl group An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. @@ -5147,14 +3501,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus @@ -5162,7 +3522,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + elemental oxygen elemental oxygen @@ -5173,7 +3533,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rare earth metal atom rare earth metal atom @@ -5184,7 +3544,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -5196,7 +3556,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium atom gadolinium atom @@ -5207,7 +3567,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + terbium atom terbium atom @@ -5220,7 +3580,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), <small>D</small>-ribose or 2-deoxy-<small>D</small>-ribose and phosphoric acid. nucleic acid @@ -5242,7 +3602,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amino acid A carboxylic acid containing one or more amino groups. @@ -5254,7 +3614,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer @@ -5267,7 +3627,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hemoglobin hemoglobin @@ -5278,7 +3638,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -5290,7 +3650,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium molecular entity gadolinium molecular entity @@ -5301,7 +3661,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -5310,10 +3670,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A particle smaller than an atom. + subatomic particle + + + + - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5325,9 +3696,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more <small>L</small>-glutamic acid units. folic acids @@ -5337,7 +3708,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium phosphate sodium phosphate @@ -5348,7 +3719,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5367,7 +3738,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5376,7 +3747,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin <small><sup>1</small></sup>/<small><sub>2</sub></small>. phosphorus-33 atom @@ -5456,7 +3827,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5467,7 +3838,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium ion calcium ion @@ -5478,7 +3849,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + magnesium cation Any magnesium ion that is positively charged. @@ -5510,7 +3881,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + A hydroxy steroid that consists of 5β-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3β-, 12β- and 14β-positions. It has been isolated from the plant species of the genus <em>Digitalis</em>. digoxigenin @@ -5520,7 +3891,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -5532,7 +3903,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + deoxyribonucleotide A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. @@ -5544,9 +3915,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + A cardenolide glycoside that is digitoxin β-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, <em>Digitalis lanata</em>, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. digoxin @@ -5567,7 +3938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -5579,7 +3950,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -5591,7 +3962,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -5603,15 +3974,26 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of γ rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 + + + + + resorufin + + resorufin + + + + @@ -5667,7 +4049,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -5679,7 +4061,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -5691,7 +4073,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -5703,7 +4085,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -5715,9 +4097,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two <em>N</em>-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5727,9 +4109,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent. N-methylisatoic anhydride @@ -5739,9 +4121,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (<i>S</i>)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5751,7 +4133,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -5763,9 +4145,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue @@ -5775,7 +4157,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -5787,7 +4169,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -5799,7 +4181,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -5811,7 +4193,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + thyroid stimulating hormone thyroid stimulating hormone @@ -5822,7 +4204,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Luteinizing hormone Luteinizing hormone @@ -5833,7 +4215,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Follicle stimulating hormone Follicle stimulating hormone @@ -5844,9 +4226,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + A hydroxycalciol that is vitamin D<small><sub>2</sub></small> in which the hydrogen at position 25 has been replaced by a hydroxy group. 25-hydroxyvitamin D2 @@ -5856,9 +4238,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + A primary amino compound that is <em>tert</em>-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7—9; p<em>K</em><small><sub>a</sub></small> = 8.3 at 20 °C; p<em>K</em><small><sub>a</sub></small> = 7.82 at 37 °C. tris @@ -5980,24 +4362,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + + cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. cell line cell - - - - - - - - - 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. - @@ -6109,10 +4487,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell @@ -6276,6 +4656,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte + A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. + + oligodendrocyte + + + + @@ -6437,11 +4829,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + experimentally modified cell in vitro @@ -6612,10 +5003,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mononuclear cell + mononuclear leukocyte A leukocyte with a single non-segmented nucleus in the mature form. - mononuclear cell + mononuclear leukocyte @@ -6692,14 +5083,297 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + - complex of molecules - A complex of two or more molecular entities that are not covalently bound. - - complex of molecules + + + + + + + A complex of two or more molecules that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A completely executed planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device @@ -6740,6 +5414,36 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental system process + + + + @@ -7014,7 +5718,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -7205,7 +5911,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RNA nuclease activity - Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + Catalysis of the cleavage of phosphodiester bonds in chains of RNA. RNA nuclease activity @@ -7227,6 +5933,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). @@ -7296,6 +6011,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of DNA repair + Any process that modulates the frequency, rate or extent of DNA repair. + + regulation of DNA repair + + + + @@ -7320,6 +6047,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + apoptotic process + A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. + + apoptotic process + + + + @@ -7344,6 +6083,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + plasma membrane organization + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + + plasma membrane organization + + + + @@ -7368,6 +6119,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryo implantation + Attachment of the blastocyst to the uterine lining. + + embryo implantation + + + + @@ -7396,10 +6159,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + + biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological process biological_process @@ -7549,6 +6318,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oxidoreductase activity + Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. + + oxidoreductase activity + + + + @@ -7585,6 +6366,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytolysis + The rupture of cell membranes and the loss of cytoplasm. + + cytolysis + + + + @@ -7669,6 +6462,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron differentiation + The process in which a relatively unspecialized cell acquires specialized features of a neuron. + + neuron differentiation + + + + + + + + + neuron projection development + The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). + + neuron projection development + + + + @@ -8190,7 +7007,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + @@ -8200,6 +7018,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. protein complex protein-containing complex @@ -8375,6 +7194,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hormone biosynthetic process + The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone biosynthetic process + + + + + + + + + hormone catabolic process + The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone catabolic process + + + + @@ -8439,6 +7282,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron projection + A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. + + neuron projection + + + + @@ -8475,6 +7330,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + @@ -8511,6 +7376,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + DNA-templated DNA replication maintenance of fidelity + A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair. + + DNA-templated DNA replication maintenance of fidelity + + + + @@ -8523,6 +7400,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synapse + The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. + + synapse + + + + @@ -8535,6 +7424,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte differentiation + The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. + + oligodendrocyte differentiation + + + + + + + + + anatomical structure development + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. + + anatomical structure development + + + + @@ -8607,6 +7520,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryonic process involved in female pregnancy + A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. + + embryonic process involved in female pregnancy + + + + + + + + + estrous cycle phase + The progression of physiological phases, occurring in the endometrium during the estrous cycle that recur at regular intervals during the reproductive years. The estrous cycle is an ovulation cycle where the endometrium is resorbed if pregnancy does not occur. + + estrous cycle phase + + + + @@ -8835,6 +7772,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of synapse maturation + Any process that modulates the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state. + + regulation of synapse maturation + + + + @@ -8967,6 +7916,37 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + neuron projection arborization + The process in which the anatomical structures of a neuron projection are generated and organized into branches. A neuron projection is any process extending from a neural cell, such as axons or dendrites. + + neuron projection arborization + + + + @@ -8991,6 +7971,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + mitotic DNA replication maintenance of fidelity + Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication. + + mitotic DNA replication maintenance of fidelity + + + + @@ -9015,6 +8007,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Severity + The intensity or degree of a manifestation. + + Severity + + + + @@ -9063,6 +8067,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + @@ -9116,9 +8130,10 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. + Pier: 'data, information or knowledge'. OR 'representation' information content entity @@ -9625,7 +8640,7 @@ clustering algorithm. - + documenting A planned process in which a document is created or added to by including the specified input in it. @@ -9650,7 +8665,7 @@ points together with a line. - + assigning a centrally registered identifier A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity @@ -10021,6 +9036,17 @@ No imports + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + @@ -10415,7 +9441,7 @@ No imports - + Viruses Viruses @@ -10560,10 +9586,19 @@ No imports + + + + + cellular organism + + + + - + Treponema pallidum Treponema pallidum @@ -10585,7 +9620,7 @@ No imports - + Bacteria eubacteria @@ -10597,7 +9632,7 @@ No imports - + Archaea Archaea @@ -10644,7 +9679,7 @@ No imports - + Eukaryota eucaryotes eukaryotes @@ -10753,6 +9788,17 @@ No imports + + + + + Pseudomonadati + + Pseudomonadati + + + + @@ -10982,7 +10028,7 @@ No imports - + Orientia tsutsugamushi Orientia tsutsugamushi @@ -11060,7 +10106,7 @@ No imports - + biological attribute biological attribute @@ -11223,30 +10269,21 @@ No imports - - - - - - - - - - - - - planned process + + obsolete planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + obsolete planned process + true @@ -11529,7 +10566,7 @@ objectives is a planned process. - + drug role @@ -11549,7 +10586,7 @@ objectives is a planned process. - + @@ -11584,7 +10621,7 @@ objectives is a planned process. - + physical document a book is a physical document @@ -11615,24 +10652,16 @@ objectives is a planned process. - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + obsolete processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + PERSON: Alan Ruttenberg + + + obsolete processed material + true @@ -11919,7 +10948,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -11934,7 +10963,7 @@ objectives is a planned process. - + @@ -12041,7 +11070,21 @@ objectives is a planned process. - + + + + + + + + + + + + + + + @@ -12127,7 +11170,7 @@ objectives is a planned process. - + @@ -12190,7 +11233,7 @@ objectives is a planned process. - + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 @@ -12332,38 +11375,21 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - - - - - - - - - - - - - - - - - material processing + + obsolete material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters + PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + OBI branch derived + + + obsolete material processing + true @@ -12478,7 +11504,7 @@ editor = PRS - + @@ -12867,7 +11893,7 @@ specimen can later be subject. - + @@ -13602,7 +12628,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13690,7 +12716,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13986,7 +13012,7 @@ for now. - + @@ -14028,10 +13054,16 @@ for now. + + + + + + plan The plan of researcher X to perform an experiment according to a protocol. - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived @@ -14193,8 +13225,8 @@ for now. - - + + @@ -14273,7 +13305,7 @@ for now. - + @@ -14372,14 +13404,14 @@ for now. - + - + @@ -14442,7 +13474,7 @@ need to add mobile phase as role - + @@ -14515,7 +13547,6 @@ need to add mobile phase as role - @@ -14629,7 +13660,7 @@ Proposal is to obsolete. - + @@ -14791,7 +13822,7 @@ Proposal is to obsolete. - + @@ -15143,7 +14174,7 @@ Proposal is to obsolete. - + @@ -15207,7 +14238,7 @@ Proposal is to obsolete. - + @@ -15468,7 +14499,7 @@ Proposal is to obsolete. - + @@ -15687,7 +14718,7 @@ activity) - + @@ -15708,7 +14739,7 @@ activity) - + @@ -16081,7 +15112,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16243,7 +15274,6 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra @@ -16258,7 +15288,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16327,7 +15357,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16627,7 +15657,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16737,7 +15767,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16747,7 +15777,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + manufacturing @@ -16950,7 +15980,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16963,7 +15993,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. @@ -17152,7 +16182,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -17366,7 +16396,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -17382,7 +16412,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -17689,7 +16719,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -17841,7 +16871,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18201,7 +17231,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18433,7 +17463,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -18802,13 +17832,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -19699,15 +18729,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - @@ -19775,26 +18796,55 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -20229,7 +19279,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20272,11 +19322,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + device setting @@ -20375,7 +19425,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20383,7 +19433,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20850,7 +19900,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + whole organism preparation @@ -21278,7 +20328,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21288,13 +20338,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + animal feeding @@ -21454,7 +20504,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21469,7 +20519,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21741,14 +20791,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -21811,7 +20861,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21879,7 +20929,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21905,7 +20955,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22057,7 +21107,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22081,7 +21131,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22211,7 +21261,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. @@ -22306,7 +21356,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + host role @@ -22526,7 +21576,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. @@ -22580,7 +21630,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22605,7 +21655,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs @@ -22630,13 +21680,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - - - + cloning vector @@ -22783,7 +21831,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site @@ -23255,6 +22302,7 @@ the role 'adjuvant role' inheres in some 'material entity' a + @@ -23489,11 +22537,11 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23565,7 +22613,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23598,7 +22646,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23689,14 +22737,14 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23765,7 +22813,6 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA Amplied DNA created by PCR @@ -23780,7 +22827,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23813,24 +22860,15 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule + true @@ -23884,7 +22922,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution @@ -23921,7 +22959,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -23935,7 +22973,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24193,7 +23231,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24214,7 +23252,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + pill A dose of medicine or placebo in the form of a small pellet. @@ -24273,7 +23311,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24281,7 +23319,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + measurement device A ruler, a microarray scanner, a Geiger counter. @@ -24406,7 +23444,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. @@ -24418,6 +23456,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -24446,7 +23485,7 @@ placeholder - + @@ -24474,7 +23513,7 @@ placeholder - + @@ -24495,7 +23534,7 @@ placeholder - + @@ -24577,23 +23616,14 @@ placeholder - - - - - - - - - - - - - primary structure of RNA molecule + + obsolete primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters - primary structure of RNA molecule + + obsolete primary structure of RNA molecule + true @@ -25144,7 +24174,7 @@ placeholder - + @@ -25467,7 +24497,7 @@ Person: Chris Stoeckert - + @@ -25478,7 +24508,7 @@ Person: Chris Stoeckert - + @@ -25884,7 +24914,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26031,7 +25061,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26055,7 +25085,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - + @@ -26773,8 +25803,8 @@ Updated both textual and logical definition. Both input and output material of f - + labeled specimen A specimen that has been modified in order to be able to detect it in future experiments @@ -26794,7 +25824,7 @@ Updated both textual and logical definition. Both input and output material of f - + infectious agent is a material entity bearing the disposition to infect an organism @@ -26903,7 +25933,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26955,7 +25985,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26963,7 +25993,7 @@ Updated both textual and logical definition. Both input and output material of f - + material separation device flow cytometer @@ -27045,7 +26075,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27122,7 +26152,7 @@ Updated both textual and logical definition. Both input and output material of f - + training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility @@ -27225,7 +26255,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27238,7 +26268,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27351,7 +26381,7 @@ Biochimie. 2010 Feb 18. - + service provider role @@ -27521,14 +26551,14 @@ Biochimie. 2010 Feb 18. - + - + processed specimen @@ -27593,7 +26623,7 @@ Biochimie. 2010 Feb 18. - + @@ -27813,7 +26843,7 @@ Biochimie. 2010 Feb 18. - + @@ -27844,7 +26874,7 @@ Biochimie. 2010 Feb 18. - + @@ -27852,7 +26882,7 @@ Biochimie. 2010 Feb 18. - + container A device that can be used to restrict the location of material entities over time @@ -27866,50 +26896,21 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - device + + obsolete device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - device + + + obsolete device + true @@ -27989,11 +26990,11 @@ In the examples above, a reagent is an operational component of a device, but th - + - + @@ -28004,7 +27005,7 @@ In the examples above, a reagent is an operational component of a device, but th sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data @@ -28111,7 +27112,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28531,7 +27532,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28853,7 +27854,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -28945,7 +27946,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -29332,7 +28333,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -29349,7 +28350,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30083,7 +29084,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30091,7 +29092,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) @@ -30109,7 +29110,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30117,7 +29118,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + perturbation device A homogenizer is a perturbation device. @@ -30137,7 +29138,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30153,7 +29154,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + environmental control device A growth chamber is an environmental control device. @@ -30446,7 +29447,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30532,7 +29533,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30629,7 +29630,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30731,7 +29732,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30751,7 +29752,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30797,7 +29798,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30823,7 +29824,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30883,7 +29884,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31032,7 +30033,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31052,7 +30053,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31283,7 +30284,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31355,7 +30356,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31457,7 +30458,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31477,7 +30478,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31651,7 +30652,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31719,7 +30720,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31864,7 +30865,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31918,7 +30919,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31978,7 +30979,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32046,7 +31047,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32066,7 +31067,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32126,7 +31127,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32365,7 +31366,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32418,7 +31419,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + individual organism identifier @@ -32577,7 +31578,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32676,7 +31677,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. @@ -32819,7 +31820,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -32830,7 +31831,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -33150,7 +32151,7 @@ All subtype will be defined by textual definition now. - + @@ -33166,11 +32167,11 @@ All subtype will be defined by textual definition now. - + - + service @@ -33320,15 +32321,6 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - @@ -33468,13 +32460,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -33486,7 +32478,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms @@ -37726,7 +36718,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -38335,7 +37327,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -40990,32 +39982,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - + genetic characteristics information @@ -43395,7 +42362,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -43424,7 +42391,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44305,7 +43272,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44361,7 +43328,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46020,10 +44987,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + @@ -46044,30 +45011,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + @@ -46727,7 +45684,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + material processing service @@ -47182,7 +46139,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + DNA sequence data @@ -49290,7 +48247,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 @@ -57712,7 +56669,7 @@ is realized in a specimen collection process. - + @@ -58378,7 +57335,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59378,7 +58335,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59730,7 +58687,7 @@ PMID: 23587118. - + @@ -59816,11 +58773,11 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - + - + reagent @@ -60824,7 +59781,7 @@ The following are NOT conclusions based on data: data themselves; results from p - + cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. @@ -61926,7 +60883,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. @@ -62006,7 +60963,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -62142,7 +61099,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay @@ -62298,7 +61255,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -62520,7 +61477,7 @@ PMID: 23587118. - + freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. @@ -62683,7 +61640,7 @@ PMID: 23587118. - + @@ -62718,7 +61675,7 @@ PMID: 23587118. - + @@ -62966,7 +61923,7 @@ PMID: 23587118. - + @@ -63205,7 +62162,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63213,7 +62170,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63276,7 +62233,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63287,7 +62244,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64575,6 +63532,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -64689,6 +63670,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -65665,7 +64670,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -65695,7 +64700,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -67343,11 +66348,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + @@ -70590,7 +69595,7 @@ https://www.doi.org/ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -70705,7 +69710,7 @@ https://www.doi.org/ - + determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. @@ -71707,7 +70712,7 @@ https://www.doi.org/ - + delivery form for hormonal replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. @@ -72310,7 +71315,7 @@ https://www.doi.org/ - + @@ -72321,7 +71326,7 @@ https://www.doi.org/ - + @@ -72884,11 +71889,11 @@ https://www.doi.org/ - + - + @@ -72909,11 +71914,11 @@ https://www.doi.org/ - + - + @@ -73264,7 +72269,7 @@ https://www.doi.org/ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. @@ -76336,7 +75341,7 @@ https://www.doi.org/ - + @@ -76358,7 +75363,7 @@ https://www.doi.org/ - + machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. @@ -78593,7 +77598,7 @@ https://www.doi.org/ 1 - + @@ -78660,7 +77665,7 @@ https://www.doi.org/ - + @@ -78668,7 +77673,7 @@ https://www.doi.org/ - + @@ -78691,7 +77696,7 @@ https://www.doi.org/ - + @@ -78713,7 +77718,7 @@ https://www.doi.org/ - + @@ -81919,7 +80924,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -81927,7 +80932,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + molecular label @@ -82001,7 +81006,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. @@ -82125,7 +81130,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA @@ -82893,7 +81898,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -83079,7 +82084,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -83185,7 +82190,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -83333,7 +82338,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + specimen collection device A device used to collect a specimen. @@ -83402,7 +82407,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -83466,7 +82471,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -83838,7 +82843,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + arthropod trap A device designed to catch arthropods. @@ -83897,7 +82902,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -83957,7 +82962,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + dipper for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. @@ -85421,11 +84426,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -85591,7 +84596,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. @@ -85607,7 +84612,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. @@ -86312,8 +85317,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + @@ -86701,7 +85705,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -86709,7 +85713,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87016,7 +86020,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87037,7 +86041,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. @@ -87414,7 +86418,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + common name of organism @@ -87502,7 +86506,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87513,7 +86517,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -88421,7 +87425,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -90922,7 +89926,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre leukapheresis - A blood harvesting process in which white blood cells are separated from a blood specimen. + A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis @@ -92822,7 +91826,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. @@ -93723,7 +92727,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -93731,7 +92735,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -94652,7 +93656,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf @@ -96267,7 +95271,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -97825,7 +96829,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -98314,7 +97318,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100728,7 +99732,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100736,7 +99740,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100759,7 +99763,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100850,7 +99854,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100858,7 +99862,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100881,7 +99885,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100972,7 +99976,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100980,7 +99984,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -101003,7 +100007,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -102928,14 +101932,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -102948,7 +101952,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasting @@ -102988,7 +101992,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasted @@ -103266,15 +102270,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - @@ -103357,7 +102352,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103791,7 +102785,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103833,7 +102827,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103874,7 +102868,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103942,7 +102936,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103966,7 +102960,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104022,7 +103016,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104033,7 +103027,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104080,7 +103074,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104091,7 +103085,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104138,7 +103132,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104149,7 +103143,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104196,7 +103190,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104207,7 +103201,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104254,7 +103248,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104265,7 +103259,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104312,7 +103306,2360 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + reproductive assay + + A physical examination of an organism that provides information about some reproductive process in that organism. + Jennifer Fostel + reproductive assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + vital sign assay + + An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). + Jennifer Fostel + vital sign assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood pressure assay + + A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. + Jennifer Fostel + blood pressure assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + heart rate variability assay + + A pulse rate assay that measures beat to beat variability in heart beats. + Jennifer Fostel + heart rate variability assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pulse rate assay + + A vital sign assay that measures the heart beat rate of an organism. + Jennifer Fostel + pulse rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + respiratory assay + + A vital sign assay that measures the quality of respiration / respiratory system of an organism + Jennifer Fostel + respiratory assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell differentiation assay + + A cytometry assay that monitors the differentiation stage of cells in culture. + Jennifer Fostel + cell differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell based DNA damage assay + + A cytometry assay that measures DNA damage in cells. + Jennifer Fostel + cell based DNA damage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell count assay + + A cytometry assay to determine the number of natural killer cells in a specimen + Jennifer Fostel + natural killer cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell percentage assay + + A cytometry assay that measures the percentage of natural killer cells in a specimen. + Jennifer Fostel + natural killer cell percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sperm count assay + + A cytometry assay to count the number of mature sperm in a specimen. + Jennifer Fostel + sperm count assay + + + + + + + + + survey administration assay + + An assay that obtains data from one or more participants by using a survey or questionnaire + Jennifer Fostel + survey administration assay + + + + + + + + + maximum data transformation + + A data transformation that has as its output the greatest value in the input data set. + Sebastian Duesing + maximum data transformation + + + + + + + + + minimum data transformation + + A data transformation that has as its output the least value in the input data set. + Sebastian Duesing + minimum data transformation + + + + + + + + + + + + + + + + + + + + + + + + + clinical history collection assay + A clinician asking a patient about the patient's smoking status. + + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. + Sebastian Duesing + HCC + clinical history collection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + disease severity assay + Measuring bone mineral density to determine the severity of osteoporosis. + + An assay that measures the severity of a disease in an organism. + Sebastian Duesing + HCC + disease severity assay + + + + + + + + + + + + + + + genetic characteristic assay + Determining a patient's HLA type. + + An assay that produces information about a genetic characteristic of an organism. + Sebastian Duesing + HCC + genetic characteristic assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood type assay + Identifying a person's ABO blood type. + + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. + Sebastian Duesing + https://medlineplus.gov/ency/article/003345.htm + blood type assay + + + + + + + + + manual muscle testing 8 score + + A clinical data item that quantifies the muscle function of a person based on the person's ability to hold a series of eight body positions that target different muscle groups. + Sebastian Duesing + MMT-8 + https://www.niehs.nih.gov/sites/default/files/research/resources/assets/docs/mmt8_grading_and_testing_procedures_for_the_abbreviated_8_muscle_groups_508.pdf + manual muscle testing 8 score + + + + + + + + + childhood myositis assessment scale score + + A clinical data item that quantifies the degree of muscle function in a child with myositis based on performance of 14 tasks associated with muscular strength and endurance. + Sebastian Duesing + CMAS + https://pubmed.ncbi.nlm.nih.gov/10524696/ + childhood myositis assessment scale score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary electrophoresis mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. + Sebastian Duesing + CE-MS + Thomas Payne + https://en.wikipedia.org/wiki/Capillary_electrophoresis–mass_spectrometry + https://github.com/obi-ontology/obi/issues/1904 + Thomas Payne + capillary electrophoresis mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite outgrowth assay + + A cell differentiation assay that detects neurite outgrowth and/or branching + The UBERON term for neurite is Neuron projection (GO:0043005; A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.). Multiplexed fluorescent imaging can be used to detect nuclei in neuronal cell bodies using Hoechst dye and neurites using anti-beta III-tubulin antibody staining. Commonly measured are neurite length, number and/or number of branch points (arborization). + Jennifer Fostel + neurite outgrowth assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuronal differentiation assay + + A cell differentiation assay that measures differentiation of neurons. + Jennifer Fostel + neuronal differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte differentiation assay + + A cell differentiation assay that measures differentiation of oligodendrocytes. + Jennifer Fostel + oligodendrocyte differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + regulation of synapse maturation assay + + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. + Synaptic puncta is this context is a small (0.5 to 2 um) distinct localized cluster of proteins involved in synaptic transmission. + Jennifer Fostel + regulation of synapse maturation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ames assay + + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. + The bacterial strains were originally constructed by Bruce Ames. Each carries a mutation in a gene involved in histidine synthesis. The cell requires histidine for growth but cannot produce it. The assay measures the creation of mutations that result in a return of function so that the cells can grow on a histidine-free medium. + Jennifer Fostel + Ames assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + micronucleus assay + + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. + The GO term "micronucleus" (GO:0031040) applies to protozoa but does not pertain to this case. Here micronucleus is a chromosome or fragment of a chromosome bounded by nuclear membrane that did not segregate properly at mitosis. + Jennifer Fostel + micronucleus assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PIG-a assay + + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. + The Pig-A gene encodes a product involved in biosynthesis of cell surface anchor glycosylphosphatidylinositol (GPI). + Jennifer Fostel + PIG-a assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin + + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. + Resazurin is the active ingredient in alamar blue; has a blue color and is non-fluorescent. Resorufin has pink color and is fluorescent. Detection of resorufin can be by absorbance or fluorescence. + Jennifer Fostel + Alamar Blue viability assay + cell viability assay based on detection of resorufin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using caspase abundance to detect apoptosis + + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis + Caspases 3 and 7 are frequently used as indicators of apoptosis. + Jennifer Fostel + cell death assay using caspase abundance to detect apoptosis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay + + A cell viability assay which measures the number or proportion of dead cells in a population. + Jennifer Fostel + cell death assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin + Resazurin (active ingredient in alamar blue and CellTiter blue reagents) has a blue color and is not fluorescent. Resorufin is pink and fluorescent. This assay uses the commercial reagent CellTiter Blue (Promega) containing resazurin and fluorescence to detect resorufin. + Jennifer Fostel + CellTiter Blue viability assay + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release + + A cell death assay that measures the release of intracellular LDH. + Jennifer Fostel + cell death assay detecting lactate dehydrogenase (LDH) release + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate + In this assay reagents are added so that LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate, and the NADH converts a tetrazolium salt to a colored formazan product in the presence of an electron acceptor. This formazan product is detected by absorbance quality. + Jennifer Fostel + Cytotox 96 assay + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ovulation assessment in rodent assay + + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. + Jennifer Fostel + Corpus luteum count + ovulation assessment in rodent assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + macroscopic examination of material anatomical entity assay + + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. + Jennifer Fostel + macroscopic examination of material anatomical entity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pathological macroscopic examination of specimen assay + + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. + one objective of this assay is to provide information about the character and extent of changes present and to inform on the cause of death. + Jennifer Fostel + Gross pathology assessment + pathological macroscopic examination of specimen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle assay based on tissue morphology + + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. + Jennifer Fostel + estrous cycle assay based on tissue morphology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo + + An organism development assay performed with a late embryo stage subject. + one objective of this assay is to assess anatomical structures and identify developmental phenotype + Jennifer Fostel + fetal examination + organism development assay in late embryo + + + + + + + + + + + + + + + + + + + + @@ -104323,7 +105670,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104341,24 +105688,26 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - reproductive assay + pregnancy assessment based on tissue morphology assay - A physical examination of an organism that provides information about some reproductive process in that organism. + A histological assay that measures the number of implantation sites in an organism. + An implantation site in this context is the site in the endometrium where the fertilized egg attaches and embeds itself to begin development Jennifer Fostel - reproductive assay + implantation site count + pregnancy assessment based on tissue morphology assay - + - - + + @@ -104370,7 +105719,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104381,7 +105730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104399,24 +105748,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - vital sign assay + cell death assay using vital dye - An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. + Living cells exclude Trypan blue Jennifer Fostel - vital sign assay + cell death assay using vital dye - + - - + + @@ -104428,7 +105778,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104439,7 +105789,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104451,30 +105801,44 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + - + - blood pressure assay + neurite length assay - A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. + A neurite is a neuronal process greater than 10 um extending from a neuron. Jennifer Fostel - blood pressure assay + neurite length assay - + - - + + @@ -104486,7 +105850,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104497,7 +105861,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104511,8 +105875,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + + + + + + + + @@ -104521,24 +105892,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - heart rate variability assay + neurite degree of arborization assay - A pulse rate assay that measures beat to beat variability in heart beats. + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes Jennifer Fostel - heart rate variability assay + neurite branch point count + neurite degree of arborization assay - + - - + + @@ -104550,7 +105922,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104561,7 +105933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104575,8 +105947,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + + + + + + + + + @@ -104585,24 +105964,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - pulse rate assay + neurite count assay - A vital sign assay that measures the heart beat rate of an organism. + A cytometry assay that measures the number of neurites in a cultured specimen. + A neurite is a neuronal process greater than 10 um extending from a neuron. Jennifer Fostel - pulse rate assay + neurite count assay - + - - + + @@ -104614,7 +105994,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104625,7 +106005,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104639,34 +106019,30 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - + - - - - + + + + + + - respiratory assay + neuron count assay - A vital sign assay that measures the quality of respiration / respiratory system of an organism + A cytometry assay that measures the number of neurons in a sample Jennifer Fostel - respiratory assay + neuron count assay - + - - + + @@ -104678,7 +106054,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104689,7 +106065,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104701,30 +106077,68 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - cell differentiation assay + cell-body-associated presynaptic puncta count assay - A cytometry assay that monitors the differentiation stage of cells in culture. + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - cell differentiation assay + cell-body-associated presynaptic puncta count assay - + - - + + @@ -104736,7 +106150,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104747,7 +106161,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104767,10 +106181,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -104778,35 +106192,49 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + - + - cell based DNA damage assay + dendrite-associated presynaptic puncta count assay - A cytometry assay that measures DNA damage in cells. + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - cell based DNA damage assay + dendrite-associated presynaptic puncta count assay - + - - + + @@ -104818,7 +106246,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104829,7 +106257,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104841,30 +106269,44 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + - + - natural killer cell count assay + synapse per neuron assay - A cytometry assay to determine the number of natural killer cells in a specimen + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. Jennifer Fostel - natural killer cell count assay + synapse per neuron assay - + - - + + @@ -104876,7 +106318,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104887,7 +106329,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104905,24 +106347,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - natural killer cell percentage assay + absorbance quality detection assay - A cytometry assay that measures the percentage of natural killer cells in a specimen. + An assay that measures the absorbance quality of the evaluant + the unit of this assay is absorbance unit (UO:0000269) Jennifer Fostel - natural killer cell percentage assay + absorbance quality detection assay - + - - + + @@ -104931,10 +106374,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -104942,17 +106385,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + @@ -104963,29 +106396,110 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + - sperm count assay + hormone assay - A cytometry assay to count the number of mature sperm in a specimen. + The analyte assay that measures the abundance of a hormone in a specimen. Jennifer Fostel - sperm count assay + hormone assay - + - - - survey administration assay + + + electrocardiograph + + An instrument for recording the changes of electrical potential occurring during the heartbeat used especially in diagnosing abnormalities of heart action. + Jennifer Fostel + https://www.merriam-webster.com/dictionary/electrocardiograph + electrocardiograph + + + + + + + + + biotelemeter - An assay that obtains data from one or more participants by using a survey or questionnaire + A measurement device that also transmits the measurement information from a biological material to a distant station. Jennifer Fostel - survey administration assay + biotelemeter + + + + + + + + + multi-electrode array plate + + A measurement device consisting of grid of tightly spaced microscopic electrodes that can detect the electrical signals of cells in close proximity. + Multielectrode arrays can be embedded in the bottom of a well and cells can be cultured over the electrodes for passive, noninvasive monitoring of electrical activity. + Jennifer Fostel + multi-electrode array plate + + + + + + + + + Transepithelial Electrical Resistance (TEER) device + + A measurement device that measures monolayer barrier integrity via measurement of membrane potential and electrical resistance across a cell monolayer in culture. + Jennifer Fostel + Transepithelial Electrical Resistance (TEER) device + + + + + + + + + randomized clinical trial + + A clinical trial in which the participants are divided by chance into separate groups that compare different treatments or other interventions. Using chance to divide people into groups means that the groups will be similar and that the effects of the treatments they receive can be compared more fairly. At the time of the trial, it is not known which treatment is best. + Sebastian Duesing + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/randomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + randomized clinical trial + + + + + + + + + non-randomized clinical trial + + A clinical trial in which the participants are not assigned by chance to different treatment groups. Participants may choose which group they want to be in, or they may be assigned to the groups by the researchers. + Sebastian Duesing + nonrandomized clinical trial + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/nonrandomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + non-randomized clinical trial @@ -105032,7 +106546,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. @@ -105047,7 +106561,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + chimera An organism which contains cells or tissues with a different genotype @@ -105081,7 +106595,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -105155,31 +106668,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - organism - animal - fungus - plant - virus + + obsolete organism + animal + fungus + plant + virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + WEB: http://en.wikipedia.org/wiki/Organism + + + obsolete organism + true @@ -105340,7 +106844,7 @@ This issue is outside the scope of OBI. - + @@ -105350,7 +106854,7 @@ This issue is outside the scope of OBI. - + xenograft @@ -105369,7 +106873,7 @@ This issue is outside the scope of OBI. - + @@ -105484,7 +106988,7 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- - + screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] @@ -105514,7 +107018,6 @@ change biomaterial to material in definition - synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme @@ -105533,7 +107036,7 @@ DS: Is this synthetic an oxymoron to the biomaterial? - + @@ -105653,7 +107156,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + + + + + + + + + + + + + + + @@ -105685,7 +107202,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -107840,7 +109357,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - + @@ -109697,7 +111214,7 @@ determinations of compounds. - + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. @@ -109784,7 +111301,7 @@ determinations of compounds. - + @@ -109812,7 +111329,7 @@ determinations of compounds. - + @@ -110069,7 +111586,6 @@ determinations of compounds. - denatured polymer Is a polymer which has lost secondary or tertiary structure @@ -110094,7 +111610,7 @@ determinations of compounds. - + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 @@ -110188,7 +111704,6 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 @@ -110207,7 +111722,7 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - + @@ -110215,8 +111730,8 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 + - genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 @@ -110402,7 +111917,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110423,7 +111938,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110456,7 +111971,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110489,11 +112004,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + - + @@ -110538,7 +112053,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110687,7 +112202,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -110753,7 +112268,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110774,7 +112289,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110806,14 +112321,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + - + @@ -110876,7 +112391,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110904,7 +112419,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -110931,7 +112446,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. @@ -111017,7 +112532,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -111235,7 +112750,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112165,7 +113680,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112199,7 +113714,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + particle delivery vessel FC 500 particle delivery vessel @@ -112285,7 +113800,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112307,7 +113822,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112549,7 +114064,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112640,7 +114155,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112711,7 +114226,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112830,7 +114345,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113199,7 +114714,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113374,7 +114889,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113449,7 +114964,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -114107,7 +115622,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114136,14 +115651,14 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114159,7 +115674,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114213,7 +115728,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114230,13 +115745,13 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114316,7 +115831,7 @@ Relates to the creation of a class 'selection rule' - + exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. @@ -114436,7 +115951,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114463,11 +115978,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + @@ -114479,7 +115994,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114675,7 +116190,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114698,7 +116213,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114892,7 +116407,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114914,7 +116429,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114977,7 +116492,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115074,7 +116589,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115096,7 +116611,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115152,7 +116667,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115226,7 +116741,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115266,7 +116781,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115287,17 +116802,17 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + - + @@ -115383,7 +116898,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115779,7 +117294,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115874,7 +117389,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115995,7 +117510,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116110,8 +117625,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + - @@ -116139,7 +117654,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116167,7 +117682,7 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti - + @@ -116235,7 +117750,7 @@ addition of has_role restriction - + @@ -116266,7 +117781,7 @@ old defintion: A mixture (collection) of cell components created by rupturing of - + @@ -116320,7 +117835,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -116350,7 +117864,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. @@ -116675,7 +118189,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + Immunization in vivo @@ -116767,7 +118281,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116883,7 +118397,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116928,7 +118442,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116936,7 +118450,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. @@ -117204,7 +118718,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen @@ -118000,19 +119513,20 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - blood harvesting + blood specimen collection - A material separation where blood is taken from an organism. + A specimen collection in which blood is collected from an organism. IEDB + blood harvesting IEDB - blood harvesting + blood specimen collection @@ -118200,7 +119714,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen @@ -122002,7 +123515,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -147892,18 +149405,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - phenotype - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - - phenotype - - - - @@ -147960,7 +149461,7 @@ realizes some 'host of immune response role' - + treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process @@ -148044,7 +149545,7 @@ realizes some 'host of immune response role' - + parasite organism An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. @@ -148068,7 +149569,7 @@ realizes some 'host of immune response role' - + quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities @@ -148404,7 +149905,7 @@ realizes some 'host of immune response role' - + physical object quality A quality which inheres in a continuant. @@ -148413,6 +149914,30 @@ realizes some 'host of immune response role' + + + + + full-spectrum EM radiation quality + An EM radiation quality that is independent of the EM wavelength range. + + full-spectrum EM radiation quality + + + + + + + + + absorption quality + A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. + + absorption quality + + + + @@ -148918,6 +150443,16 @@ realizes some 'host of immune response role' + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + @@ -149026,12 +150561,40 @@ realizes some 'host of immune response role' + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + protein antithrombin III is a protein + An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein @@ -149279,6 +150842,16 @@ realizes some 'host of immune response role' + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + @@ -149484,6 +151057,18 @@ realizes some 'host of immune response role' + + + + + modified histone + A histone that contains one or more amino acid modifications. + + modified histone + + + + @@ -149519,7 +151104,7 @@ realizes some 'host of immune response role' - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule @@ -149807,6 +151392,18 @@ realizes some 'host of immune response role' + + + + + late embryo + An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. + + late embryo + + + + @@ -149846,7 +151443,18 @@ realizes some 'host of immune response role' + + + + + + + + + + + material anatomical entity Anatomical entity that has mass. @@ -149855,6 +151463,17 @@ realizes some 'host of immune response role' + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + @@ -150095,6 +151714,24 @@ realizes some 'host of immune response role' + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + @@ -150863,6 +152500,18 @@ realizes some 'host of immune response role' + + + + + corpus luteum + A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. + + corpus luteum + + + + @@ -151319,6 +152968,18 @@ realizes some 'host of immune response role' + + + + + phenotype + A phenotypic effect related to http://www.w3.org/2002/07/owl#Thing. + + phenotype + + + + @@ -151336,7 +152997,7 @@ realizes some 'host of immune response role' vaccination - A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. + Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response. vaccination @@ -155642,25 +157303,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - geographic location A reference to a place on the Earth, by its name or by its geographical location. @@ -155678,48 +157320,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -155742,198 +157342,9 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/src/ontology/tmp/ogms-preprocess.owl b/src/ontology/tmp/ogms-preprocess.owl index 03e7985..b95e6d3 100644 --- a/src/ontology/tmp/ogms-preprocess.owl +++ b/src/ontology/tmp/ogms-preprocess.owl @@ -1,52 +1,1175 @@ Prefix(:=) -Prefix(dce:=) +Prefix(dc:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(foaf:=) +Prefix(rdf1:=) Prefix(rdfs:=) -Prefix(dcterms:=) +Prefix(terms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) Ontology( Import() +Import() Import() Import() Import() +Import() Import() -Annotation(dcterms:description "None") -Annotation(dcterms:license ) -Annotation(dcterms:title "The Ontology for General Medical Science") - -Declaration(Class()) -Declaration(AnnotationProperty(dcterms:description)) -Declaration(AnnotationProperty(dcterms:license)) -Declaration(AnnotationProperty(dcterms:title)) +Annotation(dc:contributor "Matthew Diller"@en) +Annotation(dc:creator "Alan Ruttenberg") +Annotation(dc:creator "Albert Goldfain") +Annotation(dc:creator "Anand Kumar") +Annotation(dc:creator "Barry Smith") +Annotation(dc:creator "Bill Hogan") +Annotation(dc:creator "Brian Aevermann") +Annotation(dc:creator "Cornelius Rosse") +Annotation(dc:creator "Daniel Merico") +Annotation(dc:creator "Jie Zheng") +Annotation(dc:creator "Lindsay Cowell") +Annotation(dc:creator "Richard Scheuermann") +Annotation(dc:creator "Sivaram Arabandi") +Annotation(dc:creator "Werner Ceusters") +Annotation(dc:date "2009-08-07") +Annotation(dc:description "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. + +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."@en) +Annotation(dc:title "Ontology for General Medical Science") +Annotation(terms:license "http://creativecommons.org/licenses/by/4.0/") +Annotation(rdfs:comment "The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + +The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl + +The OGMS developer site is https://github.com/OGMS/ogms + +If you are interested in participating in the development of OGMS, please send email to matthew.diller@nih.gov"@en) + +Declaration(Class(obo:BFO_0000001)) +Declaration(Class(obo:BFO_0000015)) +Declaration(Class(obo:BFO_0000016)) +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:BFO_0000023)) +Declaration(Class(obo:BFO_0000031)) +Declaration(Class(obo:BFO_0000040)) +Declaration(Class(obo:IAO_0000027)) +Declaration(Class(obo:IAO_0000030)) +Declaration(Class(obo:OBI_0000011)) +Declaration(Class(obo:OBI_0000278)) +Declaration(Class(obo:OGMS_0000014)) +Declaration(Class(obo:OGMS_0000015)) +Declaration(Class(obo:OGMS_0000016)) +Declaration(Class(obo:OGMS_0000017)) +Declaration(Class(obo:OGMS_0000018)) +Declaration(Class(obo:OGMS_0000019)) +Declaration(Class(obo:OGMS_0000020)) +Declaration(Class(obo:OGMS_0000022)) +Declaration(Class(obo:OGMS_0000023)) +Declaration(Class(obo:OGMS_0000024)) +Declaration(Class(obo:OGMS_0000025)) +Declaration(Class(obo:OGMS_0000026)) +Declaration(Class(obo:OGMS_0000027)) +Declaration(Class(obo:OGMS_0000028)) +Declaration(Class(obo:OGMS_0000029)) +Declaration(Class(obo:OGMS_0000030)) +Declaration(Class(obo:OGMS_0000031)) +Declaration(Class(obo:OGMS_0000032)) +Declaration(Class(obo:OGMS_0000033)) +Declaration(Class(obo:OGMS_0000034)) +Declaration(Class(obo:OGMS_0000035)) +Declaration(Class(obo:OGMS_0000037)) +Declaration(Class(obo:OGMS_0000038)) +Declaration(Class(obo:OGMS_0000039)) +Declaration(Class(obo:OGMS_0000040)) +Declaration(Class(obo:OGMS_0000045)) +Declaration(Class(obo:OGMS_0000046)) +Declaration(Class(obo:OGMS_0000047)) +Declaration(Class(obo:OGMS_0000050)) +Declaration(Class(obo:OGMS_0000051)) +Declaration(Class(obo:OGMS_0000055)) +Declaration(Class(obo:OGMS_0000056)) +Declaration(Class(obo:OGMS_0000057)) +Declaration(Class(obo:OGMS_0000059)) +Declaration(Class(obo:OGMS_0000060)) +Declaration(Class(obo:OGMS_0000061)) +Declaration(Class(obo:OGMS_0000063)) +Declaration(Class(obo:OGMS_0000064)) +Declaration(Class(obo:OGMS_0000065)) +Declaration(Class(obo:OGMS_0000066)) +Declaration(Class(obo:OGMS_0000067)) +Declaration(Class(obo:OGMS_0000069)) +Declaration(Class(obo:OGMS_0000070)) +Declaration(Class(obo:OGMS_0000071)) +Declaration(Class(obo:OGMS_0000073)) +Declaration(Class(obo:OGMS_0000074)) +Declaration(Class(obo:OGMS_0000077)) +Declaration(Class(obo:OGMS_0000078)) +Declaration(Class(obo:OGMS_0000079)) +Declaration(Class(obo:OGMS_0000080)) +Declaration(Class(obo:OGMS_0000081)) +Declaration(Class(obo:OGMS_0000082)) +Declaration(Class(obo:OGMS_0000083)) +Declaration(Class(obo:OGMS_0000084)) +Declaration(Class(obo:OGMS_0000085)) +Declaration(Class(obo:OGMS_0000086)) +Declaration(Class(obo:OGMS_0000087)) +Declaration(Class(obo:OGMS_0000088)) +Declaration(Class(obo:OGMS_0000089)) +Declaration(Class(obo:OGMS_0000090)) +Declaration(Class(obo:OGMS_0000091)) +Declaration(Class(obo:OGMS_0000092)) +Declaration(Class(obo:OGMS_0000093)) +Declaration(Class(obo:OGMS_0000094)) +Declaration(Class(obo:OGMS_0000095)) +Declaration(Class(obo:OGMS_0000096)) +Declaration(Class(obo:OGMS_0000097)) +Declaration(Class(obo:OGMS_0000098)) +Declaration(Class(obo:OGMS_0000099)) +Declaration(Class(obo:OGMS_0000100)) +Declaration(Class(obo:OGMS_0000101)) +Declaration(Class(obo:OGMS_0000102)) +Declaration(Class(obo:OGMS_0000103)) +Declaration(Class(obo:OGMS_0000104)) +Declaration(Class(obo:OGMS_0000105)) +Declaration(Class(obo:OGMS_0000106)) +Declaration(Class(obo:OGMS_0000107)) +Declaration(Class(obo:OGMS_0000108)) +Declaration(Class(obo:OGMS_0000109)) +Declaration(Class(obo:OGMS_0000110)) +Declaration(Class(obo:OGMS_0000111)) +Declaration(Class(obo:OGMS_0000112)) +Declaration(Class(obo:OGMS_0000113)) +Declaration(Class(obo:OGMS_0000114)) +Declaration(Class(obo:OGMS_0000115)) +Declaration(Class(obo:OGMS_0000116)) +Declaration(Class(obo:OGMS_0000117)) +Declaration(Class(obo:OGMS_0000118)) +Declaration(Class(obo:OGMS_0000119)) +Declaration(Class(obo:OGMS_0000120)) +Declaration(Class(obo:OGMS_0000121)) +Declaration(Class(obo:OGMS_0000122)) +Declaration(Class(obo:OGMS_0000123)) +Declaration(Class(obo:OGMS_0000124)) +Declaration(Class(obo:OGMS_0000125)) +Declaration(Class(obo:OGMS_0000126)) +Declaration(Class(obo:OGMS_0000127)) +Declaration(Class(obo:OGMS_0000128)) +Declaration(Class(obo:OGMS_0000129)) +Declaration(Class(obo:OGMS_0000130)) +Declaration(Class(obo:OGMS_0000131)) +Declaration(Class(obo:OGMS_0000132)) +Declaration(Class(obo:OGMS_0000133)) +Declaration(Class(obo:OGMS_0000134)) +Declaration(Class(obo:OGMS_0000135)) +Declaration(Class(obo:OGMS_0000136)) +Declaration(Class(obo:OGMS_0000137)) +Declaration(Class(obo:OGMS_0000138)) +Declaration(Class(obo:OGMS_0000139)) +Declaration(Class(obo:OGMS_0000140)) +Declaration(Class(obo:OGMS_0000141)) +Declaration(Class(obo:OGMS_0000142)) +Declaration(Class(obo:OGMS_0000143)) +Declaration(Class(obo:OGMS_0000144)) +Declaration(Class(obo:OGMS_0000145)) +Declaration(Class(obo:OGMS_0000146)) +Declaration(Class(obo:OGMS_0000147)) +Declaration(Class(obo:OGMS_0000148)) +Declaration(Class(obo:OGMS_0000149)) +Declaration(Class(obo:OGMS_0000150)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000116)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(obo:IAO_0000119)) +Declaration(AnnotationProperty(obo:IAO_0000232)) +Declaration(AnnotationProperty(dc:creator)) +Declaration(AnnotationProperty(dc:date)) +Declaration(AnnotationProperty(dc:description)) +Declaration(AnnotationProperty(dc:publisher)) +Declaration(AnnotationProperty(dc:title)) +Declaration(AnnotationProperty(terms:license)) + + ############################ -# Annotation Properties +# Classes ############################ -# Annotation Property: dcterms:description (description) +# Class: obo:OGMS_0000014 (clinical finding) -AnnotationAssertion(rdfs:label dcterms:description "description") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000014 "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000014 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000014 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000014 "creation date: 2010-07-19T10:18:02Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000014 "clinical finding") +SubClassOf(obo:OGMS_0000014 obo:OGMS_0000123) -# Annotation Property: dcterms:license (license) +# Class: obo:OGMS_0000015 (clinical history) -AnnotationAssertion(rdfs:label dcterms:license "license") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000015 "A series of statements representing health-relevant qualities of a patient and of a patient's family."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000015 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000015 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000015 "creation date: 2010-07-19T10:18:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000015 "clinical history") +SubClassOf(obo:OGMS_0000015 obo:OGMS_0000123) -# Annotation Property: dcterms:title (title) +# Class: obo:OGMS_0000016 (clinical picture) -AnnotationAssertion(rdfs:label dcterms:title "title") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000016 "A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000016 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000016 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000016 "creation date: 2010-07-19T10:20:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000016 "clinical picture") +SubClassOf(obo:OGMS_0000016 obo:OGMS_0000123) +# Class: obo:OGMS_0000017 (clinical finding from image) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000017 "An interpretation of an image that is the output of a clinical evaluation and supports an inference to an assertion about some quality of a patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000017 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000017 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000017 "creation date: 2009-06-23T10:21:10Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000017 "clinical finding from image"@en) +SubClassOf(obo:OGMS_0000017 obo:OGMS_0000014) -############################ -# Classes -############################ +# Class: obo:OGMS_0000018 (laboratory finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000018 "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000018 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000018 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000018 "creation date: 2009-06-23T10:21:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000018 "laboratory finding") +SubClassOf(obo:OGMS_0000018 obo:OGMS_0000014) + +# Class: obo:OGMS_0000019 (preclinical finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000019 "A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000019 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000019 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000019 "creation date: 2009-06-23T10:22:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000019 "preclinical finding") +SubClassOf(obo:OGMS_0000019 obo:IAO_0000027) + +# Class: obo:OGMS_0000020 (symptom) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000020 "A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000020 "note: defined class") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000020 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000020 "creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06") +AnnotationAssertion(rdfs:label obo:OGMS_0000020 "symptom") +SubClassOf(obo:OGMS_0000020 obo:BFO_0000015) + +# Class: obo:OGMS_0000022 (manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000022 "A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000022 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000022 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000022 "creation date: 2009-06-23T11:12:33Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000022 "manifestation of a disease") +SubClassOf(obo:OGMS_0000022 obo:BFO_0000019) + +# Class: obo:OGMS_0000023 (phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000023 "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000023 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000023 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000023 "creation date: 2010-07-19T11:13:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000023 "phenotype") +SubClassOf(obo:OGMS_0000023 obo:BFO_0000019) + +# Class: obo:OGMS_0000024 (obsolete_sign) + +AnnotationAssertion(rdfs:comment obo:OGMS_0000024 "The class sign has been replaced by three seperate classes which reflect the different types of signs possible.") +AnnotationAssertion(rdfs:label obo:OGMS_0000024 "obsolete_sign") +AnnotationAssertion(owl:deprecated obo:OGMS_0000024 "true"^^xsd:boolean) + +# Class: obo:OGMS_0000025 (clinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000025 "A manifestation of a disease that is detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000025 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000025 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000025 "creation date: 2009-06-23T11:15:43Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000025 "clinical manifestation of a disease") +SubClassOf(obo:OGMS_0000025 obo:OGMS_0000022) + +# Class: obo:OGMS_0000026 (preclinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000026 "A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000026 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000026 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000026 "creation date: 2009-06-23T11:16:50Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000026 "preclinical manifestation of a disease") +SubClassOf(obo:OGMS_0000026 obo:OGMS_0000022) + +# Class: obo:OGMS_0000027 (clinical phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000027 "A clinically abnormal phenotype."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000027 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000027 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000027 "creation date: 2009-06-23T11:18:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000027 "clinical phenotype") +SubClassOf(obo:OGMS_0000027 obo:OGMS_0000023) + +# Class: obo:OGMS_0000028 (disease phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000028 "A clinically abnormal phenotype that is characteristic of a single disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000028 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000028 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000028 "creation date: 2009-06-23T11:18:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000028 "disease phenotype") +SubClassOf(obo:OGMS_0000028 obo:OGMS_0000023) + +# Class: obo:OGMS_0000029 (vital sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000029 "A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000029 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000029 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000029 "creation date: 2009-06-23T11:19:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000029 "vital sign") +SubClassOf(obo:OGMS_0000029 obo:OGMS_0000129) + +# Class: obo:OGMS_0000030 (predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000030 "A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000030 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000030 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000030 "creation date: 2009-06-23T11:20:25Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000030 "predisposition to disease of type X") +SubClassOf(obo:OGMS_0000030 obo:BFO_0000016) + +# Class: obo:OGMS_0000031 (disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000031 "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000031 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000031 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000031 "creation date: 2009-06-23T11:21:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000031 "disease") +SubClassOf(obo:OGMS_0000031 obo:BFO_0000016) + +# Class: obo:OGMS_0000032 (homeostasis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000032 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000032 "creation date: 2009-06-23T11:22:01Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000032 "homeostasis") +SubClassOf(obo:OGMS_0000032 obo:BFO_0000016) + +# Class: obo:OGMS_0000033 (genetic predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000033 "A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000033 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000033 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000033 "creation date: 2009-06-23T11:23:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000033 "genetic predisposition to disease of type X") +SubClassOf(obo:OGMS_0000033 obo:OGMS_0000030) + +# Class: obo:OGMS_0000034 (acquired genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000034 "A disease whose physical basis is an acquired genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000034 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000034 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000034 "creation date: 2009-06-23T11:24:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000034 "acquired genetic disease") +SubClassOf(obo:OGMS_0000034 obo:OGMS_0000031) + +# Class: obo:OGMS_0000035 (constitutional genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000035 "A disease whose physical basis is a constitutional genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000035 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000035 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000035 "creation date: 2009-06-23T11:24:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000035 "constitutional genetic disease") +SubClassOf(obo:OGMS_0000035 obo:OGMS_0000031) + +# Class: obo:OGMS_0000037 (altered homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000037 "Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000037 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000037 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000037 "creation date: 2009-06-23T11:26:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000037 "altered homeostasis") +SubClassOf(obo:OGMS_0000037 obo:OGMS_0000032) + +# Class: obo:OGMS_0000038 (normal homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000038 "Homeostasis of a type that is not clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000038 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000038 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000038 "creation date: 2009-06-23T11:27:28Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000038 "normal homeostasis") +SubClassOf(obo:OGMS_0000038 obo:OGMS_0000032) + +# Class: obo:OGMS_0000039 (configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000039 "A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000039 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000039 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000039 "creation date: 2009-06-23T11:36:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000039 "configuration") +SubClassOf(obo:OGMS_0000039 obo:BFO_0000019) + +# Class: obo:OGMS_0000040 (pathological physical configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000040 "A configuration which deviates in some way from a canonical configuration for a particular organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000040 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000040 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000040 "creation date: 2009-06-23T11:36:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000040 "pathological physical configuration") +SubClassOf(obo:OGMS_0000040 obo:OGMS_0000039) + +# Class: obo:OGMS_0000045 (disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000045 "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000045 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000045 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000045 "creation date: 2009-06-23T11:39:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000045 "disorder") +SubClassOf(obo:OGMS_0000045 obo:BFO_0000040) + +# Class: obo:OGMS_0000046 (epigenetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000046 "A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000046 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000046 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000046 "creation date: 2009-06-23T11:40:27Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000046 "epigenetic disorder") +SubClassOf(obo:OGMS_0000046 obo:OGMS_0000045) + +# Class: obo:OGMS_0000047 (genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000047 "A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000047 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000047 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000047 "creation date: 2009-06-23T11:41:14Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000047 "genetic disorder") +SubClassOf(obo:OGMS_0000047 obo:OGMS_0000045) + +# Class: obo:OGMS_0000050 (acquired genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000050 "A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000050 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000050 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000050 "creation date: 2009-06-23T11:43:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000050 "acquired genetic disorder") +SubClassOf(obo:OGMS_0000050 obo:OGMS_0000047) + +# Class: obo:OGMS_0000051 (constitutional genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000051 "A genetic disorder inherited during conception that is part of all cells in the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000051 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000051 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000051 "creation date: 2009-06-23T11:43:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000051 "constitutional genetic disorder") +SubClassOf(obo:OGMS_0000051 obo:OGMS_0000047) + +# Class: obo:OGMS_0000055 (clinical history taking) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000055 "A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000055 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000055 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000055 "creation date: 2009-06-23T11:49:16Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000055 "clinical history taking") +SubClassOf(obo:OGMS_0000055 obo:OGMS_0000108) + +# Class: obo:OGMS_0000056 (clinical laboratory test) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000056 "A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000056 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000056 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000056 "creation date: 2009-06-23T11:49:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000056 "clinical laboratory test") +SubClassOf(obo:OGMS_0000056 obo:OGMS_0000108) + +# Class: obo:OGMS_0000057 (physical examination) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000057 "A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000057 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000057 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000057 "creation date: 2010-07-19T11:50:18Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000057 "physical examination") +SubClassOf(obo:OGMS_0000057 obo:OGMS_0000108) + +# Class: obo:OGMS_0000059 (etiological process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000059 "A process in an organism that leads to a subsequent disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000059 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000059 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000059 "creation date: 2009-06-23T11:53:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000059 "etiological process") +SubClassOf(obo:OGMS_0000059 obo:BFO_0000015) + +# Class: obo:OGMS_0000060 (bodily process) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000060 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000060 "creation date: 2009-06-23T11:53:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000060 "bodily process") +SubClassOf(obo:OGMS_0000060 obo:BFO_0000015) + +# Class: obo:OGMS_0000061 (pathological bodily process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000061 "A bodily process that is clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000061 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000061 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000061 "creation date: 2009-06-23T11:54:29Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000061 "pathological bodily process") +SubClassOf(obo:OGMS_0000061 obo:OGMS_0000060) + +# Class: obo:OGMS_0000063 (disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000063 "The totality of all processes through which a given disease instance is realized."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000063 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000063 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000063 "creation date: 2009-06-23T11:55:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000063 "disease course") +SubClassOf(obo:OGMS_0000063 obo:BFO_0000015) + +# Class: obo:OGMS_0000064 (chronic disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000064 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000064 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000064 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000064 "creation date: 2009-06-23T11:56:26Z + +10212020 + +for definition use: +http://purl.obolibrary.org/obo/PATO_0001863") +AnnotationAssertion(rdfs:label obo:OGMS_0000064 "chronic disease course") +SubClassOf(obo:OGMS_0000064 obo:OGMS_0000063) + +# Class: obo:OGMS_0000065 (progressive disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000065 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000065 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000065 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000065 "creation date: 2009-06-23T11:57:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000065 "progressive disease course") +SubClassOf(obo:OGMS_0000065 obo:OGMS_0000063) + +# Class: obo:OGMS_0000066 (transient disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000066 "A disease course that terminates in a return to normal homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000066 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000066 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000066 "creation date: 2009-06-23T11:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000066 "transient disease course") +SubClassOf(obo:OGMS_0000066 obo:OGMS_0000063) + +# Class: obo:OGMS_0000067 (_undefined primitive term) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000067 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000067 "creation date: 2009-06-23T11:58:22Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000067 "_undefined primitive term") +SubClassOf(obo:OGMS_0000067 obo:BFO_0000001) + +# Class: obo:OGMS_0000069 (clinically abnormal) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000069 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000069 "creation date: 2009-06-23T11:59:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000069 "clinically abnormal") +SubClassOf(obo:OGMS_0000069 obo:OGMS_0000067) + +# Class: obo:OGMS_0000070 (physical basis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000070 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000070 "creation date: 2009-06-23T12:00:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000070 "physical basis") +SubClassOf(obo:OGMS_0000070 obo:OGMS_0000067) + +# Class: obo:OGMS_0000071 (realization) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000071 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000071 "creation date: 2009-06-23T12:00:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000071 "realization") +SubClassOf(obo:OGMS_0000071 obo:OGMS_0000067) + +# Class: obo:OGMS_0000073 (diagnosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000073 "The representation of a conclusion of a diagnostic process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000073 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000073 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000073 "creation date: 2009-06-23T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000073 "diagnosis") +SubClassOf(obo:OGMS_0000073 obo:OGMS_0000123) + +# Class: obo:OGMS_0000074 (normal value) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000074 "A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000074 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000074 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000074 "creation date: 2009-06-26T10:31:34Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000074 "normal value") +SubClassOf(obo:OGMS_0000074 obo:BFO_0000031) + +# Class: obo:OGMS_0000077 (pathological formation) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000077 "pathological formation") +SubClassOf(obo:OGMS_0000077 obo:BFO_0000040) + +# Class: obo:OGMS_0000078 (pathological anatomical structure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000078 "An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000078 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000078 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000078 "creation date: 2009-07-13T02:14:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000078 "pathological anatomical structure") +SubClassOf(obo:OGMS_0000078 obo:BFO_0000040) + +# Class: obo:OGMS_0000079 (portion of pathological body substance) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000079 "portion of pathological body substance") +SubClassOf(obo:OGMS_0000079 obo:BFO_0000040) + +# Class: obo:OGMS_0000080 (pathological transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000080 "A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000080 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000080 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000080 "creation date: 2009-07-13T02:17:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000080 "pathological transformation") +SubClassOf(obo:OGMS_0000080 obo:OGMS_0000061) + +# Class: obo:OGMS_0000081 (pathological derivation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000081 "A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000081 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000081 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000081 "creation date: 2009-07-13T02:17:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000081 "pathological derivation") +SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061) + +# Class: obo:OGMS_0000082 (pathological invasion) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000082 "pathological invasion") +SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061) + +# Class: obo:OGMS_0000083 (physical examination finding) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding") +SubClassOf(obo:OGMS_0000083 obo:OGMS_0000014) + +# Class: obo:OGMS_0000084 (organism population) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000084 "An aggregate of organisms of the same type."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000084 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000084 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000084 "organism population") +SubClassOf(obo:OGMS_0000084 obo:BFO_0000040) + +# Class: obo:OGMS_0000085 (pain) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000085 "A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000085 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000085 "https://philarchive.org/rec/SMITAO-12") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000085 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000085 "pain") +SubClassOf(obo:OGMS_0000085 obo:OGMS_0000020) + +# Class: obo:OGMS_0000086 (syndrome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000086 "A pattern of signs and symptoms that typically co-occur."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000086 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000086 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000086 "syndrome") +SubClassOf(obo:OGMS_0000086 obo:BFO_0000019) + +# Class: obo:OGMS_0000087 (extended organism) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000087 "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000087 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000087 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000087 "extended organism") +SubClassOf(obo:OGMS_0000087 obo:BFO_0000040) + +# Class: obo:OGMS_0000088 (patient symptom report) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000088 "A communication from a patient about something they perceive as being abnormal about their body or life."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000088 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000088 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000088 "patient symptom report") +SubClassOf(obo:OGMS_0000088 obo:IAO_0000030) + +# Class: obo:OGMS_0000089 (congenital disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000089 "A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000089 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000089 "congenital malformation") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000089 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000089 "congenital disorder") +SubClassOf(obo:OGMS_0000089 obo:BFO_0000040) + +# Class: obo:OGMS_0000090 (treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000090 "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000090 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000090 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000090 "treatment") +SubClassOf(obo:OGMS_0000090 obo:OGMS_0000096) + +# Class: obo:OGMS_0000091 (convalescence) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000091 "A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000091 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000091 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000091 "convalescence") +SubClassOf(obo:OGMS_0000091 obo:BFO_0000015) + +# Class: obo:OGMS_0000092 (life course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000092 "A process which has as parts all the processes in which a given organism is participant."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000092 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000092 "creation date: 2010-03-31T04:51:11Z + +EDIT: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000092 "life course") +SubClassOf(obo:OGMS_0000092 obo:BFO_0000015) + +# Class: obo:OGMS_0000093 (prognosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000093 "A hypothesis about some future part of a disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000093 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000093 "creation date: 2010-03-31T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000093 "prognosis") +SubClassOf(obo:OGMS_0000093 obo:IAO_0000027) + +# Class: obo:OGMS_0000094 (acute disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000094 "A disease course with an acute onset"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000094 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000094 "creation date: 2010-07-19T11:57:44Z + +10212020 + +for definition use + +http://purl.obolibrary.org/obo/PATO_0000389") +AnnotationAssertion(rdfs:label obo:OGMS_0000094 "acute disease course") +SubClassOf(obo:OGMS_0000094 obo:OGMS_0000063) + +# Class: obo:OGMS_0000095 (inflammatory process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000095 "A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000095 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000095 "creation date: 2010-07-19T11:57:44Z + +Updated: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000095 "inflammatory process") +SubClassOf(obo:OGMS_0000095 obo:OGMS_0000060) + +# Class: obo:OGMS_0000096 (health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000096 "A planned process with the objective to improve or maintain the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000096 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000096 "creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18") +AnnotationAssertion(rdfs:label obo:OGMS_0000096 "health care process") +SubClassOf(obo:OGMS_0000096 obo:OBI_0000011) + +# Class: obo:OGMS_0000097 (health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000097 "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000097 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000097 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000097 "health care encounter") +SubClassOf(obo:OGMS_0000097 obo:OGMS_0000096) + +# Class: obo:OGMS_0000098 (hospitalization) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000098 "A health care process in which a person is admitted to a hospital for treatment, diagnosis, or monitoring."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000098 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000098 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000098 "hospitalization") +SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096) + +# Class: obo:OGMS_0000099 (outpatient encounter) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter") +SubClassOf(obo:OGMS_0000099 obo:OGMS_0000097) + +# Class: obo:OGMS_0000100 (inpatient encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000100 "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000100 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000100 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000100 "inpatient encounter") +SubClassOf(obo:OGMS_0000100 obo:OGMS_0000097) + +# Class: obo:OGMS_0000101 (emergency department encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000101 "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000101 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000101 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000101 "emergency department encounter") +SubClassOf(obo:OGMS_0000101 obo:OGMS_0000097) + +# Class: obo:OGMS_0000102 (injury) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000102 "A disorder that involves some structural damage that is immediately caused by a catastrophic external force."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000102 "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000102 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000102 "creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000102 "injury") +SubClassOf(obo:OGMS_0000102 obo:OGMS_0000045) + +# Class: obo:OGMS_0000103 (disease prophylaxis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000103 "A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000103 "Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000103 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000103 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000103 "disease prophylaxis") +SubClassOf(obo:OGMS_0000103 obo:OBI_0000011) + +# Class: obo:OGMS_0000104 (diagnostic process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000104 "A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000104 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000104 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000104 "diagnostic process") +SubClassOf(obo:OGMS_0000104 obo:OGMS_0000096) + +# Class: obo:OGMS_0000105 (relapse) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000105 "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000105 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000105 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000105 "recurrent") +AnnotationAssertion(dc:date obo:OGMS_0000105 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000105 "relapse"@en) +SubClassOf(obo:OGMS_0000105 obo:OBI_0000278) + +# Class: obo:OGMS_0000106 (remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000106 "A disease stage which is characterized by the lack of a manifestation of a disease") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000106 "A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000106 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(dc:date obo:OGMS_0000106 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000106 "remission"@en) +SubClassOf(obo:OGMS_0000106 obo:OBI_0000278) + +# Class: obo:OGMS_0000107 (ancillary health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000107 "A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient.") +AnnotationAssertion(dc:date obo:OGMS_0000107 "2017-04-18") +AnnotationAssertion(dc:publisher obo:OGMS_0000107 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000107 "ancillary health care process") +SubClassOf(obo:OGMS_0000107 obo:OBI_0000011) + +# Class: obo:OGMS_0000108 (health care process assay) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000108 "A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.") +AnnotationAssertion(dc:date obo:OGMS_0000108 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000108 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000108 "health care process assay") +SubClassOf(obo:OGMS_0000108 obo:OGMS_0000096) + +# Class: obo:OGMS_0000109 (health care process biomaterial transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000109 "A health care process which results in physical changes in a specified input material") +AnnotationAssertion(dc:date obo:OGMS_0000109 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000109 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000109 "health care process biomaterial transformation") +SubClassOf(obo:OGMS_0000109 obo:OGMS_0000096) + +# Class: obo:OGMS_0000110 (health care process data transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000110 "A health care process that produces output from input data") +AnnotationAssertion(dc:date obo:OGMS_0000110 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000110 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000110 "health care process data transformation") +SubClassOf(obo:OGMS_0000110 obo:OGMS_0000096) + +# Class: obo:OGMS_0000111 (prophylactic treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000111 "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000111 "Creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000111 "prophylactic treatment"@en) +SubClassOf(obo:OGMS_0000111 obo:OGMS_0000090) + +# Class: obo:OGMS_0000112 (therapeutic procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000112 "A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000112 "Creation data: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000112 "therapeutic procedure"@en) +SubClassOf(obo:OGMS_0000112 obo:OGMS_0000090) + +# Class: obo:OGMS_0000113 (chemotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000113 "A therapeutic procedure that uses synthetic or naturally-occurring chemicals") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000113 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000113 "chemotherapy procedure"@en) +SubClassOf(obo:OGMS_0000113 obo:OGMS_0000112) + +# Class: obo:OGMS_0000114 (immunotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000114 "A therapeutic procedure that uses immune system derived entities.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000114 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000114 "immunotherapy procedure"@en) +SubClassOf(obo:OGMS_0000114 obo:OGMS_0000112) + +# Class: obo:OGMS_0000115 (physical therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000115 "A therapeutic procedure that uses physical conditioning") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000115 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000115 "physical therapy procedure"@en) +SubClassOf(obo:OGMS_0000115 obo:OGMS_0000112) + +# Class: obo:OGMS_0000116 (radiation therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000116 "A therapeutic procedure that uses radiation.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000116 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000116 "radiation therapy procedure"@en) +SubClassOf(obo:OGMS_0000116 obo:OGMS_0000112) + +# Class: obo:OGMS_0000117 (asymptomatic) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000117 "A disease stage characterized by the lack of symptoms associated with a given disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000117 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000117 "asymptomatic"@en) +SubClassOf(obo:OGMS_0000117 obo:OBI_0000278) + +# Class: obo:OGMS_0000118 (onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000118 "A disease stage that marks the beginning of a disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000118 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000118 "onset"@en) +SubClassOf(obo:OGMS_0000118 obo:OBI_0000278) + +# Class: obo:OGMS_0000119 (acute onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000119 "A disease stage with a rapid unfolding of signs and symptoms") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000119 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000119 "acute onset"@en) +SubClassOf(obo:OGMS_0000119 obo:OGMS_0000118) + +# Class: obo:OGMS_0000120 (complete remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000120 "A remission which is characterized by a prolonged lack of all manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000120 "complete remission"@en) +SubClassOf(obo:OGMS_0000120 obo:OGMS_0000106) + +# Class: obo:OGMS_0000121 (partial remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000121 "A remission which is characterized by a prolonged lack of some manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000121 "partial remission"@en) +SubClassOf(obo:OGMS_0000121 obo:OGMS_0000106) + +# Class: obo:OGMS_0000122 (recovered from disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000122 "A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000122 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000122 "recovered from disease"@en) +SubClassOf(obo:OGMS_0000122 obo:BFO_0000019) + +# Class: obo:OGMS_0000123 (clinical data item) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000123 "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000123 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000123 "clinical data item"@en) +SubClassOf(obo:OGMS_0000123 obo:IAO_0000027) + +# Class: obo:OGMS_0000124 (routine health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000124 "A health care encounter that is regularly scheduled for the purpose of health monitoring.") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000124 "routine clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000124 "routine health care encounter") +SubClassOf(obo:OGMS_0000124 obo:OGMS_0000099) + +# Class: obo:OGMS_0000125 (follow-up health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000125 "A health care encounter that is scheduled for the purpose of assessing a known set of specific issues") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000125 "follow-up clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000125 "follow-up health care encounter") +SubClassOf(obo:OGMS_0000125 obo:OGMS_0000099) + +# Class: obo:OGMS_0000126 (congenital infection) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000126 "A congenital disorder arising as a result of an infectious process") +AnnotationAssertion(rdfs:label obo:OGMS_0000126 "congenital infection") +SubClassOf(obo:OGMS_0000126 obo:OGMS_0000089) + +# Class: obo:OGMS_0000127 (drug induced congenital malformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000127 "A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality") +AnnotationAssertion(rdfs:label obo:OGMS_0000127 "drug induced congenital malformation") +SubClassOf(obo:OGMS_0000127 obo:OGMS_0000089) + +# Class: obo:OGMS_0000128 (congenital process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000128 "A pathological bodily process that occurs in the fetus during fetal development") +AnnotationAssertion(rdfs:label obo:OGMS_0000128 "congenital process") +SubClassOf(obo:OGMS_0000128 obo:OGMS_0000061) + +# Class: obo:OGMS_0000129 (physical sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000129 "An abnormal material entity that is part of a patient and hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000129 "Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension") +AnnotationAssertion(rdfs:label obo:OGMS_0000129 "physical sign") +SubClassOf(obo:OGMS_0000129 obo:BFO_0000040) + +# Class: obo:OGMS_0000130 (allergic disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000130 "The process in which an allergic disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000130 "allergic disease process") +SubClassOf(obo:OGMS_0000130 obo:OGMS_0000061) + +# Class: obo:OGMS_0000131 (cancer process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000131 "The process in which cancer unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000131 "cancer process") +SubClassOf(obo:OGMS_0000131 obo:OGMS_0000061) + +# Class: obo:OGMS_0000132 (autoimmune disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000132 "The process in which an autoimmune disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000132 "autoimmune disease process") +SubClassOf(obo:OGMS_0000132 obo:OGMS_0000061) + +# Class: obo:OGMS_0000133 (progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000133 "progression stage") +SubClassOf(obo:OGMS_0000133 obo:OBI_0000278) + +# Class: obo:OGMS_0000134 (cancer progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000134 "cancer progression stage") +SubClassOf(obo:OGMS_0000134 obo:OGMS_0000133) + +# Class: obo:OGMS_0000135 (cancer progression stage 0) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000135 "A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ).") +AnnotationAssertion(rdfs:label obo:OGMS_0000135 "cancer progression stage 0") +SubClassOf(obo:OGMS_0000135 obo:OGMS_0000134) + +# Class: obo:OGMS_0000136 (cancer progression stage I) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000136 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000136 "cancer progression stage I") +SubClassOf(obo:OGMS_0000136 obo:OGMS_0000134) + +# Class: obo:OGMS_0000137 (cancer progression stage II) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000137 "A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000137 "cancer progression stage II") +SubClassOf(obo:OGMS_0000137 obo:OGMS_0000134) + +# Class: obo:OGMS_0000138 (cancer progression stage III) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000138 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000138 "cancer progression stage III") +SubClassOf(obo:OGMS_0000138 obo:OGMS_0000134) + +# Class: obo:OGMS_0000139 (cancer progression stage IV) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000139 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000139 "cancer progression stage IV") +SubClassOf(obo:OGMS_0000139 obo:OGMS_0000134) + +# Class: obo:OGMS_0000140 (infectious disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000140 "The process in which an infectious disease unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000140 "infectious disease process") +SubClassOf(obo:OGMS_0000140 obo:OGMS_0000061) + +# Class: obo:OGMS_0000141 (processual sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000141 "An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(rdfs:label obo:OGMS_0000141 "processual sign") +SubClassOf(obo:OGMS_0000141 obo:BFO_0000015) + +# Class: obo:OGMS_0000142 (qualitative sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000142 "An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000142 "Example: the color of a rash; the shape of a melanoma") +AnnotationAssertion(rdfs:label obo:OGMS_0000142 "qualitative sign") +SubClassOf(obo:OGMS_0000142 obo:BFO_0000019) + +# Class: obo:OGMS_0000143 (transplantation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000143 "A therapeutic procedure in which a body part is transferred into a organism") +AnnotationAssertion(rdfs:label obo:OGMS_0000143 "transplantation") +SubClassOf(obo:OGMS_0000143 obo:OGMS_0000112) + +# Class: obo:OGMS_0000144 (solid organ transplant) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000144 "A transplantation in which the body part is a non-fluid tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000144 "solid organ transplant") +SubClassOf(obo:OGMS_0000144 obo:OGMS_0000143) + +# Class: obo:OGMS_0000145 (transfusion) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000145 "A transplantation in which the body part is a bodily fluid") +AnnotationAssertion(rdfs:label obo:OGMS_0000145 "transfusion") +SubClassOf(obo:OGMS_0000145 obo:OGMS_0000143) + +# Class: obo:OGMS_0000146 (tissue disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000146 "A disorder of some macroscopic part of a tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000146 "tissue disorder") +SubClassOf(obo:OGMS_0000146 obo:OGMS_0000045) + +# Class: obo:OGMS_0000147 (neoplasm) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000147 "A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass") +AnnotationAssertion(rdfs:label obo:OGMS_0000147 "neoplasm") +SubClassOf(obo:OGMS_0000147 obo:OGMS_0000146) + +# Class: obo:OGMS_0000148 (medication role) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000148 "A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000148 "Originally OBIB_0000026") +AnnotationAssertion(rdfs:label obo:OGMS_0000148 "medication role") +SubClassOf(obo:OGMS_0000148 obo:BFO_0000023) + +# Class: obo:OGMS_0000149 (patient-reported outcome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000149 "A data item that is about a patient’s health that comes directly from the patient. A patient reported outcome can include subjective feelings regarding symptoms, functions in daily life, physical, mental, emotional, spiritual, and social well-being, and satisfaction with healthcare that has been received."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000149 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000149 "https://www.cancer.gov/publications/dictionaries/cancer-terms/def/patient-reported-outcome") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(oboInOwl:hasBroadSynonym obo:OGMS_0000149 "PRO"@en) +AnnotationAssertion(rdfs:comment obo:OGMS_0000149 "The outcome does not necessarily need to be related to a healthcare intervention. For example, it can be about a patient's overall quality of life related to a disease."@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000149 "patient-reported outcome"@en) +SubClassOf(obo:OGMS_0000149 obo:IAO_0000027) -# Class: (root node) +# Class: obo:OGMS_0000150 (healthcare outcome report) -AnnotationAssertion(rdfs:label "root node"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000150 "A data item about a persont's health status or condition resulting from healthcare interventions, treatments, or services."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000150 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(rdfs:label obo:OGMS_0000150 "healthcare outcome report"@en) +SubClassOf(obo:OGMS_0000150 obo:IAO_0000027) ) \ No newline at end of file diff --git a/src/ontology/tmp/pre_seed.txt b/src/ontology/tmp/pre_seed.txt index f9d7dac..61db557 100644 --- a/src/ontology/tmp/pre_seed.txt +++ b/src/ontology/tmp/pre_seed.txt @@ -1,7 +1,147 @@ term -https://creativecommons.org/licenses/unspecified -http://purl.obolibrary.org/obo/OGMS_0000000 -http://purl.org/dc/terms/license -http://purl.org/dc/terms/description -http://purl.org/dc/terms/title +http://purl.obolibrary.org/obo/BFO_0000001 +http://purl.obolibrary.org/obo/OGMS_0000106 +http://purl.obolibrary.org/obo/BFO_0000019 +http://purl.obolibrary.org/obo/OBI_0000278 +http://purl.obolibrary.org/obo/BFO_0000015 +http://purl.obolibrary.org/obo/OGMS_0000045 +http://purl.obolibrary.org/obo/OGMS_0000060 +http://purl.obolibrary.org/obo/OGMS_0000030 +http://purl.obolibrary.org/obo/BFO_0000031 +http://purl.obolibrary.org/obo/OGMS_0000014 +http://purl.obolibrary.org/obo/BFO_0000040 +http://purl.obolibrary.org/obo/OGMS_0000061 +http://purl.obolibrary.org/obo/OGMS_0000090 +http://purl.obolibrary.org/obo/OGMS_0000099 +http://purl.obolibrary.org/obo/OGMS_0000039 +http://purl.obolibrary.org/obo/OGMS_0000134 +http://purl.obolibrary.org/obo/OGMS_0000022 +http://purl.obolibrary.org/obo/OGMS_0000063 +http://purl.obolibrary.org/obo/OGMS_0000032 +http://purl.obolibrary.org/obo/OGMS_0000096 +http://purl.obolibrary.org/obo/OGMS_0000143 +http://purl.obolibrary.org/obo/BFO_0000016 +http://purl.obolibrary.org/obo/OGMS_0000123 +http://purl.obolibrary.org/obo/OGMS_0000097 +http://purl.obolibrary.org/obo/IAO_0000027 +http://purl.obolibrary.org/obo/OBI_0000011 +http://purl.obolibrary.org/obo/OGMS_0000112 +http://purl.obolibrary.org/obo/OGMS_0000020 +http://purl.obolibrary.org/obo/OGMS_0000108 +http://purl.obolibrary.org/obo/OGMS_0000129 +http://purl.obolibrary.org/obo/OGMS_0000047 +http://purl.obolibrary.org/obo/OGMS_0000067 +http://purl.obolibrary.org/obo/OGMS_0000023 +http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/OGMS_0000031 +http://purl.obolibrary.org/obo/OGMS_0000089 +http://purl.obolibrary.org/obo/OGMS_0000133 +http://purl.obolibrary.org/obo/OGMS_0000146 +http://purl.obolibrary.org/obo/OGMS_0000118 +http://purl.obolibrary.org/obo/IAO_0000030 +http://purl.obolibrary.org/obo/OGMS_0000120 +http://purl.obolibrary.org/obo/IAO_0000117 +http://purl.obolibrary.org/obo/OGMS_0000105 http://purl.obolibrary.org/obo/ogms.owl +http://purl.obolibrary.org/obo/OGMS_0000033 +http://purl.obolibrary.org/obo/OGMS_0000074 +http://purl.obolibrary.org/obo/OGMS_0000046 +http://purl.obolibrary.org/obo/OGMS_0000018 +http://purl.obolibrary.org/obo/OGMS_0000087 +http://purl.obolibrary.org/obo/OGMS_0000140 +http://purl.obolibrary.org/obo/OGMS_0000059 +http://purl.obolibrary.org/obo/OGMS_0000125 +http://purl.org/dc/terms/license +http://purl.obolibrary.org/obo/OGMS_0000040 +http://purl.obolibrary.org/obo/OGMS_0000138 +http://purl.obolibrary.org/obo/OGMS_0000081 +http://purl.obolibrary.org/obo/OGMS_0000025 +http://purl.obolibrary.org/obo/OGMS_0000094 +http://purl.obolibrary.org/obo/OGMS_0000066 +http://purl.obolibrary.org/obo/OGMS_0000038 +http://purl.obolibrary.org/obo/OGMS_0000079 +http://purl.obolibrary.org/obo/IAO_0000116 +http://purl.obolibrary.org/obo/OGMS_0000132 +http://purl.obolibrary.org/obo/OGMS_0000104 +http://purl.obolibrary.org/obo/OGMS_0000145 +http://purl.obolibrary.org/obo/OGMS_0000117 +http://purl.obolibrary.org/obo/OGMS_0000073 +http://purl.obolibrary.org/obo/OGMS_0000017 +http://purl.obolibrary.org/obo/OGMS_0000086 +http://purl.obolibrary.org/obo/OGMS_0000111 +http://purl.obolibrary.org/obo/OGMS_0000124 +http://purl.obolibrary.org/obo/OGMS_0000137 +http://purl.obolibrary.org/obo/OGMS_0000080 +http://purl.obolibrary.org/obo/OGMS_0000109 +http://purl.obolibrary.org/obo/OGMS_0000024 +http://purl.org/dc/elements/1.1/description +http://purl.obolibrary.org/obo/OGMS_0000093 +http://purl.obolibrary.org/obo/OGMS_0000065 +http://purl.org/dc/elements/1.1/publisher +http://purl.obolibrary.org/obo/OGMS_0000037 +http://purl.obolibrary.org/obo/OGMS_0000131 +http://purl.obolibrary.org/obo/OGMS_0000078 +http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.org/dc/elements/1.1/creator +http://purl.obolibrary.org/obo/OGMS_0000103 +http://purl.obolibrary.org/obo/OGMS_0000144 +http://purl.obolibrary.org/obo/OGMS_0000116 +http://purl.obolibrary.org/obo/OGMS_0000016 +http://purl.obolibrary.org/obo/OGMS_0000085 +http://purl.obolibrary.org/obo/OGMS_0000057 +http://purl.obolibrary.org/obo/OGMS_0000110 +http://purl.obolibrary.org/obo/OGMS_0000029 +http://purl.obolibrary.org/obo/OGMS_0000098 +http://purl.obolibrary.org/obo/OGMS_0000136 +http://purl.obolibrary.org/obo/OGMS_0000051 +http://purl.obolibrary.org/obo/OGMS_0000149 +http://purl.obolibrary.org/obo/OGMS_0000092 +http://purl.obolibrary.org/obo/OGMS_0000064 +http://purl.obolibrary.org/obo/OGMS_0000077 +http://purl.obolibrary.org/obo/OGMS_0000130 +http://purl.obolibrary.org/obo/OGMS_0000102 +http://purl.obolibrary.org/obo/OGMS_0000115 +http://purl.obolibrary.org/obo/OGMS_0000128 +http://purl.obolibrary.org/obo/OGMS_0000071 +http://purl.obolibrary.org/obo/OGMS_0000015 +http://purl.obolibrary.org/obo/OGMS_0000084 +http://purl.obolibrary.org/obo/OGMS_0000056 +http://purl.obolibrary.org/obo/OGMS_0000028 +http://purl.obolibrary.org/obo/OGMS_0000150 +http://purl.obolibrary.org/obo/OGMS_0000069 +http://purl.obolibrary.org/obo/OGMS_0000122 +http://purl.obolibrary.org/obo/IAO_0000119 +http://purl.obolibrary.org/obo/OGMS_0000135 +http://purl.obolibrary.org/obo/OGMS_0000107 +http://purl.obolibrary.org/obo/OGMS_0000050 +http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym +http://purl.obolibrary.org/obo/OGMS_0000148 +http://purl.obolibrary.org/obo/OGMS_0000091 +http://purl.obolibrary.org/obo/OGMS_0000035 +http://purl.org/dc/elements/1.1/date +http://purl.obolibrary.org/obo/OGMS_0000101 +http://purl.obolibrary.org/obo/OGMS_0000142 +http://purl.obolibrary.org/obo/OGMS_0000114 +http://purl.obolibrary.org/obo/OGMS_0000127 +http://purl.obolibrary.org/obo/OGMS_0000070 +http://purl.obolibrary.org/obo/OGMS_0000083 +http://purl.obolibrary.org/obo/OGMS_0000055 +http://purl.obolibrary.org/obo/OGMS_0000027 +http://purl.obolibrary.org/obo/OGMS_0000121 +http://purl.obolibrary.org/obo/IAO_0000118 +http://purl.org/dc/elements/1.1/contributor +http://purl.obolibrary.org/obo/OGMS_0000147 +http://purl.obolibrary.org/obo/OGMS_0000119 +http://purl.obolibrary.org/obo/OGMS_0000034 +http://purl.obolibrary.org/obo/OGMS_0000100 +http://purl.obolibrary.org/obo/OGMS_0000019 +http://purl.obolibrary.org/obo/OGMS_0000088 +http://purl.obolibrary.org/obo/OGMS_0000141 +http://purl.obolibrary.org/obo/OGMS_0000113 +http://purl.obolibrary.org/obo/OGMS_0000126 +http://purl.org/dc/elements/1.1/title +http://purl.obolibrary.org/obo/IAO_0000232 +http://purl.obolibrary.org/obo/OGMS_0000139 +http://purl.obolibrary.org/obo/OGMS_0000082 +http://purl.obolibrary.org/obo/OGMS_0000026 +http://purl.obolibrary.org/obo/OGMS_0000095 diff --git a/src/ontology/tmp/ro-download.owl b/src/ontology/tmp/ro-download.owl index a3d3910..fff2d40 100644 --- a/src/ontology/tmp/ro-download.owl +++ b/src/ontology/tmp/ro-download.owl @@ -9,7 +9,6 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" - xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -17,15 +16,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2025-03-05 + 2025-12-17 https://github.com/oborel/obo-relations/ @@ -42,12 +40,6 @@ - - - - - - @@ -289,17 +281,6 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - @@ -1196,54 +1177,18 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1286,12 +1231,6 @@ Where we have an annotation assertion - - - - - - @@ -1322,30 +1261,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1366,12 +1281,6 @@ Where we have an annotation assertion - - - - - - @@ -1476,30 +1385,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1682,7 +1567,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by @@ -1788,6 +1672,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y + lacks_part + + + + + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) + lacks_plasma_membrane_part + + + + @@ -2356,9 +2258,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure. http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by + innervated by @@ -2736,7 +2643,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + <= Primitive instance level timing relation between events @@ -2753,7 +2660,6 @@ Examples include: the relationship between two channels collected simultaneously x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with @@ -2766,7 +2672,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before @@ -2779,7 +2685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends @@ -2810,7 +2716,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -2827,7 +2733,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by @@ -2840,7 +2746,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts @@ -2857,7 +2763,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts before @@ -2873,7 +2779,6 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland ends_at_start_of meets @@ -2890,7 +2795,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) @@ -2905,7 +2810,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + d during @@ -2923,7 +2828,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + o overlaps @@ -3580,13 +3485,29 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + - + + + + + + + + + + + + + + + + + @@ -3609,6 +3530,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + @@ -3617,6 +3542,18 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. @@ -4271,7 +4208,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of starts with - Chris Mungall Allen starts @@ -4289,7 +4225,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall started by starts with @@ -4361,7 +4296,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ends with - Chris Mungall ends @@ -4377,7 +4311,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall finished by ends with @@ -5017,7 +4950,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -6247,8 +6180,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. @@ -6821,6 +6754,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A relation that holds between a disease or an organism and a phenotype @@ -8257,8 +8191,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -8531,8 +8465,10 @@ the a supports either the existence of b, or the truth value of b. + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI + indicates is marker for @@ -8870,6 +8806,67 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + x is an ectomycorrhizal host of y if and only if x is a plant (Plantae) whose roots form an intercellular interface (aka Hartig net) with fungus (Fungi) y. This interface consists of highly branched hyphae forming a latticework between epidermal and cortical root cells. + + + + An ectomycorrhiza is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. The mycobiont is often from the phyla Basidiomycota and Ascomycota, and more rarely from the Zygomycota. Ectomycorrhizae form on the roots of around 2% of plant species, usually woody plants, including species from the birch, dipterocarp, myrtle, beech, willow, pine and rose families. Research on ectomycorrhizae is increasingly important in areas such as ecosystem management and restoration, forestry, and agriculture. Unlike other mycorrhizal relationships, such as arbuscular mycorrhiza and ericoid mycorrhiza, ectomycorrhizal fungi do not penetrate their host's cell wall. Instead they form an entirely intercellular interfaces known as the Hartig net, consisting of highly branched hyphae forming a latticework between epidermal and cortical root cells. + ectomycorrhizal host of + + + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + inverse of ectomycorrhizal host of + + has ectomycorrhizal host + + + + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + x is an arbuscular mycorrhizal host of y if and only if x is a vascular plant (Plantae) whose cortical cells of the roots are penetrated by fungus (Fungi) y and form arbuscules. + + + + An arbuscular mycorrhiza (AM) (plural mycorrhizae) is a type of mycorrhiza in which the symbiont fungus (Arbuscular mycorrhizal fungi, or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza (not to be confused with ectomycorrhiza). They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered. Arbuscular mycorrhizae are formed by fungi in the subphylum Glomeromycotina and some fungi from the Mucoromycotina. These subphyla, along with the Mortierellomycotina, form the phylum Mucoromycota, a sister clade of the more well-known and diverse dikaryan fungi. AM fungi help plants to capture nutrients such as phosphorus, sulfur, nitrogen and micronutrients from the soil. It is believed that the development of the arbuscular mycorrhizal symbiosis played a crucial role in the initial colonisation of land by plants and in the evolution of the vascular plants. It has been said that it is quicker to list the plants that do not form endomycorrhizae than those that do. This symbiosis is a highly evolved mutualistic relationship found between fungi and plants, the most prevalent plant symbiosis known, and AMF is found in 80% of vascular plant families in existence today. + arbuscular mycorrhizal host of + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + inverse of arbuscular mycorrhizal host of + + + has arbuscular mycorrhizal host + + + + @@ -9762,8 +9759,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9775,8 +9772,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9808,7 +9805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. @@ -9899,7 +9896,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -10855,6 +10852,24 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + The information in a blueprint specifies the dimensions of a building. + The information in a recipe specifies what interredients to use and the steps needed to prepare a meal. + The information in a software program specifies the order of computations. + A relation between information and an entity such that the information serves as a rule or guide if the entity is an occurrent, or the information serves as a model if the entity is a continuant. + + 2025-06-16T17:08:04Z + prescribes + specifies + information specifies + https://www.ontologyrepository.com/CommonCoreOntologies/prescribes + + + + @@ -10910,6 +10925,17 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + inverse of 'has symptom' + + 2025-06-16T17:42:05Z + symptom of + + + + @@ -10942,6 +10968,29 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + Inverse of information specifies. + + 2025-06-16T17:13:17Z + specified by information + + + + + + + + + Inverse relation of 'is marker for'. + + 2025-07-14T20:57:25Z + has marker + + + + @@ -11316,6 +11365,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context. + Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals. + + + has substitutable entity + + + + @@ -11437,86 +11499,321 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - This relation groups relations between diseases and any other kind of entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - - 2018-09-26T00:00:32Z - disease relationship + + + A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + provides clinical information for - + - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - - 2018-09-26T01:08:58Z - results in changes to anatomical or cellular structure + + + A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue. + An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype. + https://orcid.org/0000-0001-5809-9523 + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + diagnostic for - + - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - TODO: Add homeomorphy axiom - - - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - + + + Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression. + A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The status of 'd' refers to disease progression/remission or treatment response. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors status of - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - + - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - + + + The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates response to - - - - Similarity that results from common evolutionary origin. - - + + + + + + + + The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug. + +Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + predicts effect of + + + + + + + + + A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + prognostic for + + + + + + + + + As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + assesses toxicity of + + + + + + + + + The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates risk of developing + + + + + + + + + An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy. + A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates clinical effect of + + + + + + + + + The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors effect of + + + + + + + + + The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers: + - 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest; + - 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent; + - 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent. + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors exposure to + + + + + + + + + A polyubiquitin has_constituent_monomer some ubiquitin. + An amino acid chain has_constituent_monomer at least two amino acid residues. + A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer 'm' if and only if P has_component multiple instances of 'm' and each instance of 'm' is covalently attached to another instance of 'm'. + + Usage note: The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows the number of instances of 'm' to be indicated. + has constituent monomer + + + + + + + + + + Charged tRNA (i.e., aminoacyl-tRNA) is a tRNA that is covalently_bound_to some amino acid. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of covalent interactions. + + Such entities will colocalize at all times of the interaction. + covalently bound to + + + + + + + + + + Holo-calmodulin is a calmodulin that is non-covalently_bound_to calcium. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions. + + Such entities will colocalize at all times of the interaction. + non-covalently bound to + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + @@ -11529,7 +11826,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - + homoplasous to analogy @@ -11553,7 +11850,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - + ECO:0000075 homocracous to @@ -11579,7 +11876,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - + analogy Convergence usually implies a notion of adaptation. @@ -11602,7 +11899,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. @@ -11625,7 +11922,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - + ECO:0000071 MI:2163 @@ -11652,7 +11949,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - + homology ECO:0000080 @@ -11687,7 +11984,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - + ECO:0000067 biological homologous to @@ -11713,7 +12010,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - + atavism rudiment @@ -11737,7 +12034,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - + MeSH:Synteny SO:0000860 @@ -11764,7 +12061,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - + SO:0000854 SO:0000859 @@ -11792,7 +12089,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - + syntenic paralogous to duplicon @@ -11817,7 +12114,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - + syntenic orthologous to in syntenic orthology relationship with @@ -11839,7 +12136,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - + fractional homology partial homologous to @@ -11868,7 +12165,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - + MeSH:Structural_Homology,_Protein protein structural homologous to @@ -11892,7 +12189,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - + pseudogene SO:non_functional_homolog_of @@ -11916,7 +12213,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - + ECO:00000060 SO:0000855 @@ -11946,7 +12243,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). @@ -11970,7 +12267,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - + 1 to 1 homologous to 1:1 homology @@ -11995,7 +12292,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - + 1 to 1 orthologous to 1:1 orthology @@ -12020,7 +12317,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - + ohnologous to homoeology @@ -12044,7 +12341,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - + in-paralogous to inparalogy @@ -12068,7 +12365,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - + alloparalogy out-paralogous to @@ -12092,7 +12389,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - + pro-orthologous to in pro-orthology relationship with @@ -12115,7 +12412,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - + semi-orthologous to The converse of pro-orthologous. @@ -12139,7 +12436,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - + serial homologous to homonomy @@ -12162,7 +12459,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - + heterochronous homologous to heterochrony @@ -12186,7 +12483,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - + juvenification pedomorphosis @@ -12210,7 +12507,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - + in peramorphosis relationship with @@ -12231,7 +12528,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - + in progenesis relationship with @@ -12253,7 +12550,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - + juvenilization neotenous to @@ -12277,7 +12574,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - + mimicrous to in mimicry relationship with @@ -12300,7 +12597,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - + 1 to many orthologous to 1:many orthology @@ -12327,7 +12624,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - + many to many homologous to many-to-many homology @@ -12351,7 +12648,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - + 1 to many homologous to one-to-many homology @@ -12376,7 +12673,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - + apomorphous to synapomorphy @@ -12399,7 +12696,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - + plesiomorphous to symplesiomorphy @@ -12424,7 +12721,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - + deep genetic homology deep homologous to @@ -12451,7 +12748,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - + hemiplasous to in hemiplasy relationship with @@ -12473,7 +12770,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - + gametologous to in gametology relationship with @@ -12495,7 +12792,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - + MeSH:Chromosome_Pairing chromosomal homologous to @@ -12519,7 +12816,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - + many to many orthologous to many-to-many orthology @@ -12548,7 +12845,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - + within-species paralogous to in within-species paralogy relationship with @@ -12570,7 +12867,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - + between-species paralogous to The genes have diverged before a speciation event. @@ -12593,7 +12890,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - + post-displacement in postdisplacement relationship with @@ -12615,7 +12912,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - + in hypermorphosis relationship with @@ -12637,7 +12934,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - + synologous to in synology relationship with @@ -12661,7 +12958,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - + ECO:0000080 isoorthologous to @@ -12684,7 +12981,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - + tandem paralogous to iterative paralogy @@ -12710,7 +13007,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - + apomorphic tendency cryptic homology @@ -12742,7 +13039,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - + generative homology syngenous to @@ -12768,7 +13065,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - + 1:1 paralogy apparent 1:1 orthology @@ -12795,7 +13092,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. @@ -12819,7 +13116,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - + equivalogous to This may include examples of orthology, paralogy and xenology. @@ -12842,7 +13139,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - + interologous to in interology relationship with @@ -12865,7 +13162,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - + functional similarity in functional equivalence relationship with @@ -12888,7 +13185,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - + iterative homologous to in iterative homology relationship with @@ -12910,7 +13207,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - + duplicate xenology multiple xenology @@ -12934,7 +13231,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - + plerologous to This phenomenon is usually due to gene conversion process. @@ -12958,7 +13255,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. @@ -12983,7 +13280,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - + heterotopy in homeosis relationship with @@ -13007,7 +13304,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. @@ -13031,7 +13328,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - + axis paramorphism in paramorphism relationship with @@ -13054,7 +13351,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - + regulogous to in regulogy relationship with @@ -13446,6 +13743,38 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + completely executed planned process + + + + @@ -13462,6 +13791,16 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A processed material entity which is designed to be capable of a process. + device + + + + @@ -13487,14 +13826,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu An environmental system which can sustain and allow the growth of an ecological population. - - EcoLexicon:habitat LTER:238 SWEETRealm:Habitat - A habitat's specificity to an ecological population differentiates it from other environment classes. See Buttigieg et al. (2016; https://doi.org/10.1186/s13326-016-0097-6) for an explanation of ENVO's treatement of habitats. 3,849 of such habitat classes are available here: https://github.com/EnvironmentOntology/envo-habitats + https://en.wikipedia.org/wiki/Habitat + A habitat's specificity to an ecological population differentiates it from other environment classes. habitat + + + + An environmental system which can sustain and allow the growth of an ecological population. + EnvO:EnvO + @@ -13600,7 +13944,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3781009 Reactome:R-HSA-3788724 Reactome:R-HSA-3797226 - Reactome:R-HSA-400267 Reactome:R-HSA-4332236 Reactome:R-HSA-446877 Reactome:R-HSA-450358 @@ -13649,6 +13992,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-975118 Reactome:R-HSA-975147 Reactome:R-HSA-9758604 + Reactome:R-HSA-9766227 Reactome:R-HSA-9793444 Reactome:R-HSA-9793485 Reactome:R-HSA-9793679 @@ -13665,6 +14009,10 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9834070 Reactome:R-HSA-9861563 Reactome:R-HSA-9861640 + Reactome:R-HSA-9929350 + Reactome:R-HSA-9934753 + Reactome:R-HSA-9948301 + Reactome:R-HSA-9954721 ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity @@ -14083,12 +14431,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3797226 Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) - - - - Reactome:R-HSA-400267 - BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins - @@ -14249,7 +14591,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-69598 - Ubiquitination of phosphorylated Cdc25A + Ubiquitination of phosphorylated CDC25A @@ -14377,6 +14719,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9758604 Ubiquitination of IKBKG by TRAF6 + + + + Reactome:R-HSA-9766227 + MDM2 mediates CDH1 ubiquitination + @@ -14473,6 +14821,30 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9861640 CTLH E3 ligase ubiquitinates PKM-1 + + + + Reactome:R-HSA-9929350 + Ubiquitination of CD274 by BTRC-SCF E3-ligase complex + + + + + Reactome:R-HSA-9934753 + CBLL1 ubiquitinates CDH1 + + + + + Reactome:R-HSA-9948301 + ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit + + + + + Reactome:R-HSA-9954721 + NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide + @@ -14509,7 +14881,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z @@ -14638,44 +15009,22 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process - + - + - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - + - + assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. @@ -14694,7 +15043,6 @@ objectives is a planned process. - container A device that can be used to restrict the location of material entities over time @@ -14705,56 +15053,6 @@ objectives is a planned process. - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - @@ -14950,6 +15248,7 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 + FAO:0000001 FMA:305751 FMA:67135 GAID:781 @@ -14967,6 +15266,7 @@ This issue is outside the scope of OBI. connected biological structure UBERON:0000061 + @@ -15335,73 +15635,596 @@ This issue is outside the scope of OBI. - + - - example to be eventually removed - example to be eventually removed + + + + 2019-03-05T17:25:21Z + Western Australia Ecoregion + WWF:AA1310 + https://www.worldwildlife.org/ecoregions/aa1310 + Western Australian Mulga Shrublands Ecoregion - + - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete + + + 2019-03-05T17:51:32Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Australasia Ecoregion - + - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term + + + + 2019-03-05T17:52:41Z + Southern central Australia Ecoregion + WWF:AA1309 + https://www.worldwildlife.org/ecoregions/aa1309 + Tirari-Sturt Stony Desert Ecoregion - + - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release + + + + 2019-03-05T17:54:35Z + Eastern central Australia Ecoregion + WWF:AA1308 + https://www.worldwildlife.org/ecoregions/aa1308 + Simpson Desert Region - + - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete + + + + 2019-03-05T17:56:13Z + Western Australia Ecoregion + WWF:AA1307 + https://www.worldwildlife.org/ecoregions/aa1307 + Pilbara Shrublands Ecoregion - + - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated + + + + 2019-03-05T18:10:52Z + Western coast of Australia Ecoregion + WWF:AA1301 + https://www.worldwildlife.org/ecoregions/aa1301 + Carnarvon Xeric Shrublands Ecoregion - + - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + + + + 2019-03-05T18:12:28Z + Central Australia Ecoregion + WWF:AA1302 + https://www.worldwildlife.org/ecoregions/aa1302 + Central Ranges Xeric Shrub Ecoregion + + + + + + + + + + 2019-03-05T18:15:11Z + Western central Australia + WWF:AA1303 + https://www.worldwildlife.org/ecoregions/aa1303 + Gibson Desert Ecoregion + + + + + + + + + + 2019-03-05T18:17:15Z + Northwestern Australia + WWF:AA1304 + https://www.worldwildlife.org/ecoregions/aa1304 + The Great Sandy-Tanami Desert Ecoregion + + + + + + + + + + 2019-03-05T18:24:06Z + Southern Australia Ecoregion + WWF:AA1305 + https://www.worldwildlife.org/ecoregions/aa1305 + Great Victoria Desert Ecoregion + + + + + + + + + + 2019-03-05T18:26:16Z + Southern Australia Ecoregion + WWF:AA1306 + https://www.worldwildlife.org/ecoregions/aa1306 + Nullarbor Plains Xeric Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:01:41Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Afrotropical Ecoregion + + + + + + + + + + 2019-03-06T22:02:37Z + Southern Africa: Southern Namibia into South Africa + WWF:AT1322 + https://www.worldwildlife.org/ecoregions/at1322 + Succulent Karoo Ecoregion + + + + + + + + + + 2019-03-06T22:07:38Z + WWF:AT1321 + https://www.worldwildlife.org/ecoregions/at1321 + Arabian Peninsula: Yemen and Saudi Arabia + Yemen and Saudi Arabia Ecoregion + + + + + + + + + + 2019-03-06T22:11:38Z + WWF:AT1320 + https://www.worldwildlife.org/ecoregions/at1320 + Arabian Peninsula: Yemen, Saudi Arabia, and Oman + Yemen, Saudi Arabia, and Oman Ecoregion + + + + + + + + + + 2019-03-06T22:13:00Z + WWF:AT1319 + https://www.worldwildlife.org/ecoregions/at1319 + Somali montane xeric woodlands ecoregion + Somali Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-06T22:15:07Z + Islands east of the Horn of Africa and south of Yemen Ecoregion + WWF:AT1318 + https://www.worldwildlife.org/ecoregions/at1318 + Socotran Archipelago Ecoregion + + + + + + + + + 2019-03-06T22:18:55Z + WWF:AT1317 + https://www.worldwildlife.org/ecoregions/at1317 + Red Sea Coastal Desert Ecoregion + + + + + + + + + 2019-03-06T22:20:56Z + WWF:AT1316 + https://www.worldwildlife.org/ecoregions/at1316 + Namibian Savanna Woodland Ecoregion + + + + + + + + + 2019-03-06T22:24:28Z + Africa: Namibia Ecoregion + WWF:AT1315 + https://www.worldwildlife.org/ecoregions/at1315 + Namib Desert Ecoregion + + + + + + + + + 2019-03-06T22:26:15Z + WWF:AT1314 + https://www.worldwildlife.org/ecoregions/at1314 + Nama Karoo Ecoregion + + + + + + + + + 2019-03-06T22:28:43Z + WWF:AT1313 + https://www.worldwildlife.org/ecoregions/at1313 + Masai Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-06T22:30:23Z + WWF:AT1312 + https://www.worldwildlife.org/ecoregions/at1312 + Madagascar Succulent Woodlands Ecoregion + + + + + + + + + 2019-03-06T22:31:29Z + WWF:AT1311 + https://www.worldwildlife.org/ecoregions/at1311 + Madagascar spiny desert ecoregion + Madagascar Spiny Thickets Ecoregion + + + + + + + + + 2019-03-06T22:39:32Z + WWF:AT1310 + https://www.worldwildlife.org/ecoregions/at1310 + Africa: Coastal Namibia and Angola Ecoregion + Kaokoveld Desert Ecoregion + + + + + + + + + 2019-03-06T22:42:47Z + WWF:AT1309 + https://www.worldwildlife.org/ecoregions/at1309 + Kalahari Xeric Savanna Ecoregion + + + + + + + + + 2019-03-06T22:44:54Z + WWF:AT1308 + https://www.worldwildlife.org/ecoregions/at1308 + Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion + Ile Europa and Bassas da India Ecoregion + + + + + + + + + 2019-03-06T22:46:58Z + Eastern Africa: Somalia + WWF:AT1307 + https://www.worldwildlife.org/ecoregions/at1307 + Hobyo Grassland and Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:54:57Z + WWF:AT1306 + https://www.worldwildlife.org/ecoregions/at1306 + Arabian Peninsula: Oman and United Arab Emirates Ecoregion + Oman and United Arab Emirates Ecoregion + + + + + + + + + 2019-03-07T00:08:06Z + WWF:AT1305 + https://www.worldwildlife.org/ecoregions/at1305 + Ethiopian Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-07T00:11:29Z + WWF:AT1304 + https://www.worldwildlife.org/ecoregions/at1304 + Eritrean Coastal Desert Ecoregion + + + + + + + + + 2019-03-07T00:13:33Z + WWF:AT1303 + https://www.worldwildlife.org/ecoregions/at1303 + North central Africa: Eastern Chad and small area of western Sudan + East Saharan Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-07T00:16:12Z + WWF:AT1302 + https://www.worldwildlife.org/ecoregions/at1302 + Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion + Oman, Yemen, and Saudi Arabia Ecoregion + + + + + + + + + 2019-03-07T00:18:09Z + WWF:AT1301 + https://www.worldwildlife.org/ecoregions/at1301 + Aldabra Island Xeric Scrub Ecoregion + + + + + + + + 2019-04-26T23:38:50Z + + Indo-Malay Ecoregion + + + + + + + + + 2019-04-26T23:40:13Z + + WWF:IM1304 + Southern Asia: Western India into Pakistan + Thar Desert + + + + + + + + + 2019-04-27T00:12:51Z + + WWF:IM1303 + Southern Asia: Eastern India and western Pakistan + Northwestern Thorn Scrub Forests + + + + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + envoAtmo + envoPolar + Arctic front + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + + + + + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + envoAtmo + envoPolar + Antarctic front + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + + + + + + + + + + Stellar radiation emitted from Sol. + Solar radiation + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -15493,6 +16316,69 @@ binary, and takes no temporal argument. + + + + researcher + Nicole Vasilevsky + + + + + researcher + + + + + + Nicole Vasilevsky + + + + + + + + + researcher + Darren A. Natale + + + + + researcher + + + + + + Darren A. Natale + + + + + + + + + researcher ORCID ID = 0000-0001-5948-3092 + Marta Costa + + + + + researcher ORCID ID = 0000-0001-5948-3092 + + + + + + Marta Costa + + + + + @@ -15535,6 +16421,27 @@ binary, and takes no temporal argument. + + + + researcher + Katja S Schulz + + + + + researcher + + + + + + Katja S Schulz + + + + + @@ -15556,6 +16463,27 @@ binary, and takes no temporal argument. + + + + researcher + David P Hill + + + + + researcher + + + + + + David P Hill + + + + + @@ -15598,6 +16526,48 @@ binary, and takes no temporal argument. + + + + American epidemiologist and ontologist + Melissa Haendel + + + + + American epidemiologist and ontologist + + + + + + Melissa Haendel + + + + + + + + + researcher + Jennifer Deegan + + + + + researcher + + + + + + Jennifer Deegan + + + + + @@ -15619,6 +16589,48 @@ binary, and takes no temporal argument. + + + + researcher + Alexander D Diehl + + + + + researcher + + + + + + Alexander D Diehl + + + + + + + + + researcher + Matthew Brush + + + + + researcher + + + + + + Matthew Brush + + + + + @@ -15682,6 +16694,48 @@ binary, and takes no temporal argument. + + + + researcher + Tanya Z Berardini + + + + + researcher + + + + + + Tanya Z Berardini + + + + + + + + + researcher + Sabrina Toro + + + + + researcher + + + + + + Sabrina Toro + + + + + @@ -15703,6 +16757,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0002-5260-9315 + Patrick Ray + + + + + Researcher ORCID=0000-0002-5260-9315 + + + + + + Patrick Ray + + + + + @@ -15955,6 +17030,27 @@ binary, and takes no temporal argument. + + + + researcher + Terrence F Meehan + + + + + researcher + + + + + + Terrence F Meehan + + + + + @@ -16015,6 +17111,33 @@ binary, and takes no temporal argument. Charles Tapley Hoyt + + + + + + + researcher + Vasundra Touré + + + + + researcher + + + + + + Vasundra Touré + + + + + + + + @@ -16045,7 +17168,8 @@ binary, and takes no temporal argument. failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg failed exploratory term @@ -16073,21 +17197,26 @@ binary, and takes no temporal argument. placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. placeholder removed terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. term imported term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. term split @@ -16216,6 +17345,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Add as annotation triples in the granting ontology is allocated id range + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. @@ -16378,7 +17513,7 @@ No imports The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. out of scope @@ -16394,66 +17529,84 @@ No imports domain entity does not exist + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + 2025-06-02 + preferred label for community + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms + 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms + 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms + 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms + 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms + 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants + 2023-03-03 UK spelling synonym A synonym type for common misspellings + 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. + 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name + 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + 2023-09-30 INN International Nonproprietary Name @@ -16461,18 +17614,21 @@ No imports nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. + 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + 2023-11-01 acronym A serial number such as "12324X"; a stop sign; a written proper name such as "OBI An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 2024-03-25 has symbol @@ -16597,15 +17753,15 @@ No imports - - - + + + @@ -16616,6 +17772,7 @@ No imports + if effector directly negatively regulates X, its parent MF directly negatively regulates X @@ -16623,9 +17780,9 @@ No imports - - - + + + @@ -16634,9 +17791,9 @@ No imports - - - + + + @@ -16650,9 +17807,9 @@ No imports - - - + + + @@ -16660,6 +17817,7 @@ No imports + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16667,9 +17825,9 @@ No imports - - - + + + @@ -16678,9 +17836,9 @@ No imports - - - + + + @@ -16693,17 +17851,29 @@ No imports - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16711,9 +17881,9 @@ No imports - - - + + + @@ -16721,24 +17891,13 @@ No imports - - - + + + + - - - - - - - - - - - - - + @@ -16748,13 +17907,24 @@ No imports - - - - + + + - + + + + + + + + + + + + + @@ -16766,9 +17936,9 @@ No imports - - - + + + @@ -16776,9 +17946,10 @@ No imports - - - + + + + @@ -16792,9 +17963,9 @@ No imports - - - + + + @@ -16809,9 +17980,9 @@ No imports - - - + + + @@ -16819,9 +17990,10 @@ No imports - - - + + + + @@ -16835,9 +18007,9 @@ No imports - - - + + + @@ -16852,9 +18024,9 @@ No imports - - - + + + @@ -16862,9 +18034,10 @@ No imports - - - + + + + @@ -16878,9 +18051,9 @@ No imports - - - + + + @@ -16895,9 +18068,9 @@ No imports - - - + + + @@ -16905,9 +18078,10 @@ No imports - - - + + + + @@ -16921,9 +18095,9 @@ No imports - - - + + + @@ -16931,9 +18105,6 @@ No imports - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg @@ -16941,9 +18112,9 @@ No imports - - - + + + @@ -16952,36 +18123,12 @@ No imports - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -16992,9 +18139,9 @@ No imports - - - + + + @@ -17002,18 +18149,16 @@ No imports - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -17022,25 +18167,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -17051,9 +18183,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17061,9 +18193,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP @@ -17071,8 +18200,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17081,9 +18210,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17091,10 +18220,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -17110,9 +18238,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17127,9 +18255,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17138,37 +18266,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -17179,9 +18281,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17189,8 +18291,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction @@ -17198,9 +18298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17208,26 +18308,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17238,9 +18324,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17248,7 +18334,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg reg edge from input to regulatory subfunction @@ -17256,9 +18341,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17266,26 +18351,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17296,9 +18367,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17306,7 +18377,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct positive reg edge from input to regulatory subfunction @@ -17314,9 +18384,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17324,26 +18394,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17354,9 +18410,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17364,7 +18420,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - effector input is compound function input + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg @@ -17372,9 +18430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17383,12 +18441,36 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17400,8 +18482,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17409,17 +18491,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - Input of effector is input of its parent MF + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts - - - - + + + @@ -17428,12 +18511,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17444,9 +18540,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17454,17 +18550,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly regulates X, its parent MF directly regulates X + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP - - - - + + + @@ -17473,12 +18570,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17487,11 +18597,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - + + + + + @@ -17499,7 +18609,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17507,9 +18616,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17517,13 +18626,38 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17534,9 +18668,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17544,7 +18678,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly negatively regulates X, its parent MF directly negatively regulates X + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction @@ -17552,9 +18687,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17563,12 +18698,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17579,9 +18727,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17589,7 +18737,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct neg reg edge from input to regulatory subfunction @@ -17597,9 +18745,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17608,12 +18756,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17623,29 +18784,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct positive reg edge from input to regulatory subfunction @@ -17653,9 +18803,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17664,12 +18814,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17679,28 +18842,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + + effector input is compound function input @@ -17708,9 +18861,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17719,9 +18872,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17735,9 +18888,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17745,6 +18898,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + Input of effector is input of its parent MF @@ -17752,9 +18906,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17763,9 +18917,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17779,9 +18933,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17789,6 +18943,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly regulates X, its parent MF directly regulates X @@ -17796,9 +18951,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17807,9 +18962,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17823,9 +18978,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17833,6 +18988,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17840,9 +18996,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17851,9 +19007,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17867,9 +19023,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/src/ontology/tmp/seed.txt b/src/ontology/tmp/seed.txt index 5aa9e09..a45d13f 100644 --- a/src/ontology/tmp/seed.txt +++ b/src/ontology/tmp/seed.txt @@ -1,4 +1,10 @@ +http://purl.obolibrary.org/obo/BFO_0000001 +http://purl.obolibrary.org/obo/BFO_0000015 +http://purl.obolibrary.org/obo/BFO_0000016 +http://purl.obolibrary.org/obo/BFO_0000019 http://purl.obolibrary.org/obo/BFO_0000020 +http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000031 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000051 @@ -6,6 +12,9 @@ http://purl.obolibrary.org/obo/BFO_0000054 http://purl.obolibrary.org/obo/BFO_0000055 http://purl.obolibrary.org/obo/BFO_0000066 http://purl.obolibrary.org/obo/BFO_0000067 +http://purl.obolibrary.org/obo/COB_0000022 +http://purl.obolibrary.org/obo/IAO_0000027 +http://purl.obolibrary.org/obo/IAO_0000030 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000114 @@ -30,10 +39,128 @@ http://purl.obolibrary.org/obo/OBI_0000278 http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/OBI_0000846 http://purl.obolibrary.org/obo/OBI_0001688 -http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/OBI_0200000 http://purl.obolibrary.org/obo/OBI_0600052 -http://purl.obolibrary.org/obo/OGMS_0000000 +http://purl.obolibrary.org/obo/OGMS_0000014 +http://purl.obolibrary.org/obo/OGMS_0000015 +http://purl.obolibrary.org/obo/OGMS_0000016 +http://purl.obolibrary.org/obo/OGMS_0000017 +http://purl.obolibrary.org/obo/OGMS_0000018 +http://purl.obolibrary.org/obo/OGMS_0000019 +http://purl.obolibrary.org/obo/OGMS_0000020 +http://purl.obolibrary.org/obo/OGMS_0000022 +http://purl.obolibrary.org/obo/OGMS_0000023 +http://purl.obolibrary.org/obo/OGMS_0000024 +http://purl.obolibrary.org/obo/OGMS_0000025 +http://purl.obolibrary.org/obo/OGMS_0000026 +http://purl.obolibrary.org/obo/OGMS_0000027 +http://purl.obolibrary.org/obo/OGMS_0000028 +http://purl.obolibrary.org/obo/OGMS_0000029 +http://purl.obolibrary.org/obo/OGMS_0000030 +http://purl.obolibrary.org/obo/OGMS_0000031 +http://purl.obolibrary.org/obo/OGMS_0000032 +http://purl.obolibrary.org/obo/OGMS_0000033 +http://purl.obolibrary.org/obo/OGMS_0000034 +http://purl.obolibrary.org/obo/OGMS_0000035 +http://purl.obolibrary.org/obo/OGMS_0000037 +http://purl.obolibrary.org/obo/OGMS_0000038 +http://purl.obolibrary.org/obo/OGMS_0000039 +http://purl.obolibrary.org/obo/OGMS_0000040 +http://purl.obolibrary.org/obo/OGMS_0000045 +http://purl.obolibrary.org/obo/OGMS_0000046 +http://purl.obolibrary.org/obo/OGMS_0000047 +http://purl.obolibrary.org/obo/OGMS_0000050 +http://purl.obolibrary.org/obo/OGMS_0000051 +http://purl.obolibrary.org/obo/OGMS_0000055 +http://purl.obolibrary.org/obo/OGMS_0000056 +http://purl.obolibrary.org/obo/OGMS_0000057 +http://purl.obolibrary.org/obo/OGMS_0000059 +http://purl.obolibrary.org/obo/OGMS_0000060 +http://purl.obolibrary.org/obo/OGMS_0000061 +http://purl.obolibrary.org/obo/OGMS_0000063 +http://purl.obolibrary.org/obo/OGMS_0000064 +http://purl.obolibrary.org/obo/OGMS_0000065 +http://purl.obolibrary.org/obo/OGMS_0000066 +http://purl.obolibrary.org/obo/OGMS_0000067 +http://purl.obolibrary.org/obo/OGMS_0000069 +http://purl.obolibrary.org/obo/OGMS_0000070 +http://purl.obolibrary.org/obo/OGMS_0000071 +http://purl.obolibrary.org/obo/OGMS_0000073 +http://purl.obolibrary.org/obo/OGMS_0000074 +http://purl.obolibrary.org/obo/OGMS_0000077 +http://purl.obolibrary.org/obo/OGMS_0000078 +http://purl.obolibrary.org/obo/OGMS_0000079 +http://purl.obolibrary.org/obo/OGMS_0000080 +http://purl.obolibrary.org/obo/OGMS_0000081 +http://purl.obolibrary.org/obo/OGMS_0000082 +http://purl.obolibrary.org/obo/OGMS_0000083 +http://purl.obolibrary.org/obo/OGMS_0000084 +http://purl.obolibrary.org/obo/OGMS_0000085 +http://purl.obolibrary.org/obo/OGMS_0000086 +http://purl.obolibrary.org/obo/OGMS_0000087 +http://purl.obolibrary.org/obo/OGMS_0000088 +http://purl.obolibrary.org/obo/OGMS_0000089 +http://purl.obolibrary.org/obo/OGMS_0000090 +http://purl.obolibrary.org/obo/OGMS_0000091 +http://purl.obolibrary.org/obo/OGMS_0000092 +http://purl.obolibrary.org/obo/OGMS_0000093 +http://purl.obolibrary.org/obo/OGMS_0000094 +http://purl.obolibrary.org/obo/OGMS_0000095 +http://purl.obolibrary.org/obo/OGMS_0000096 +http://purl.obolibrary.org/obo/OGMS_0000097 +http://purl.obolibrary.org/obo/OGMS_0000098 +http://purl.obolibrary.org/obo/OGMS_0000099 +http://purl.obolibrary.org/obo/OGMS_0000100 +http://purl.obolibrary.org/obo/OGMS_0000101 +http://purl.obolibrary.org/obo/OGMS_0000102 +http://purl.obolibrary.org/obo/OGMS_0000103 +http://purl.obolibrary.org/obo/OGMS_0000104 +http://purl.obolibrary.org/obo/OGMS_0000105 +http://purl.obolibrary.org/obo/OGMS_0000106 +http://purl.obolibrary.org/obo/OGMS_0000107 +http://purl.obolibrary.org/obo/OGMS_0000108 +http://purl.obolibrary.org/obo/OGMS_0000109 +http://purl.obolibrary.org/obo/OGMS_0000110 +http://purl.obolibrary.org/obo/OGMS_0000111 +http://purl.obolibrary.org/obo/OGMS_0000112 +http://purl.obolibrary.org/obo/OGMS_0000113 +http://purl.obolibrary.org/obo/OGMS_0000114 +http://purl.obolibrary.org/obo/OGMS_0000115 +http://purl.obolibrary.org/obo/OGMS_0000116 +http://purl.obolibrary.org/obo/OGMS_0000117 +http://purl.obolibrary.org/obo/OGMS_0000118 +http://purl.obolibrary.org/obo/OGMS_0000119 +http://purl.obolibrary.org/obo/OGMS_0000120 +http://purl.obolibrary.org/obo/OGMS_0000121 +http://purl.obolibrary.org/obo/OGMS_0000122 +http://purl.obolibrary.org/obo/OGMS_0000123 +http://purl.obolibrary.org/obo/OGMS_0000124 +http://purl.obolibrary.org/obo/OGMS_0000125 +http://purl.obolibrary.org/obo/OGMS_0000126 +http://purl.obolibrary.org/obo/OGMS_0000127 +http://purl.obolibrary.org/obo/OGMS_0000128 +http://purl.obolibrary.org/obo/OGMS_0000129 +http://purl.obolibrary.org/obo/OGMS_0000130 +http://purl.obolibrary.org/obo/OGMS_0000131 +http://purl.obolibrary.org/obo/OGMS_0000132 +http://purl.obolibrary.org/obo/OGMS_0000133 +http://purl.obolibrary.org/obo/OGMS_0000134 +http://purl.obolibrary.org/obo/OGMS_0000135 +http://purl.obolibrary.org/obo/OGMS_0000136 +http://purl.obolibrary.org/obo/OGMS_0000137 +http://purl.obolibrary.org/obo/OGMS_0000138 +http://purl.obolibrary.org/obo/OGMS_0000139 +http://purl.obolibrary.org/obo/OGMS_0000140 +http://purl.obolibrary.org/obo/OGMS_0000141 +http://purl.obolibrary.org/obo/OGMS_0000142 +http://purl.obolibrary.org/obo/OGMS_0000143 +http://purl.obolibrary.org/obo/OGMS_0000144 +http://purl.obolibrary.org/obo/OGMS_0000145 +http://purl.obolibrary.org/obo/OGMS_0000146 +http://purl.obolibrary.org/obo/OGMS_0000147 +http://purl.obolibrary.org/obo/OGMS_0000148 +http://purl.obolibrary.org/obo/OGMS_0000149 +http://purl.obolibrary.org/obo/OGMS_0000150 http://purl.obolibrary.org/obo/RO_0000052 http://purl.obolibrary.org/obo/RO_0000053 http://purl.obolibrary.org/obo/RO_0000056 @@ -54,9 +181,13 @@ http://purl.obolibrary.org/obo/RO_0002351 http://purl.obolibrary.org/obo/RO_0002353 http://purl.obolibrary.org/obo/RO_0002577 http://purl.obolibrary.org/obo/ogms.owl -http://purl.org/dc/terms/description +http://purl.org/dc/elements/1.1/contributor +http://purl.org/dc/elements/1.1/creator +http://purl.org/dc/elements/1.1/date +http://purl.org/dc/elements/1.1/description +http://purl.org/dc/elements/1.1/publisher +http://purl.org/dc/elements/1.1/title http://purl.org/dc/terms/license -http://purl.org/dc/terms/title +http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym http://www.w3.org/2002/07/owl#Thing -https://creativecommons.org/licenses/unspecified term diff --git a/src/sparql/equivalent-classes-violation.sparql b/src/sparql/equivalent-classes-violation.sparql new file mode 100644 index 0000000..ed5ccdd --- /dev/null +++ b/src/sparql/equivalent-classes-violation.sparql @@ -0,0 +1,14 @@ +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?baseClass ?baseLabel ?equivalentClass ?equivalentLabel WHERE +{ + ?baseClass owl:equivalentClass ?equivalentClass . + ?baseClass rdfs:label ?baseLabel . + ?equivalentClass rdfs:label ?equivalentLabel . + + FILTER (!isBlank(?baseClass)) . + FILTER (!isBlank(?equivalentClass)) + +} diff --git a/src/templates/external_import.tsv b/src/templates/external_import.tsv index 5d82db6..f94988a 100644 --- a/src/templates/external_import.tsv +++ b/src/templates/external_import.tsv @@ -33,7 +33,6 @@ OBI:0000011 owl:ObjectProperty OBI:0000312 owl:ObjectProperty OBI:0000846 owl:ObjectProperty OBI:0001688 owl:ObjectProperty -OBI:0100026 owl:Class OBI:0200000 owl:Class OBI:0600052 owl:Class RO:0000052 owl:ObjectProperty @@ -55,3 +54,4 @@ RO:0002351 owl:ObjectProperty RO:0002353 owl:ObjectProperty RO:0002577 owl:ObjectProperty RO:0002012 owl:ObjectProperty +COB:0000022 owl:Class