diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 1257681..73df362 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,26 +1,73 @@ -## Before you write a new request, please consider the following: +## Contributing to the ontology by opening tickets -- **Does the term already exist?** Before submitting suggestions for new -ontology terms, check whether the term exist, either as a primary term -or a synonym term. You can search using [OLS](http://www.ebi.ac.uk/ols/ontologies/fbbi) +The easiest way to contribute to the Biological Imaging Methods Ontology +is by opening tickets on our [issue tracker](https://github.com/foundingGIDE/fbbi/issues) +to requests new terms or amendments to existing terms. -## Guidelines for creating GitHub tickets with contributions to the ontology: +This does not require you to be familiar with ontology editing +procedures, as your request will be handled by someone in the Biological +Imaging Methods Ontology editorial team, who will do the actual editing. -1. **Write a detailed request:** Please be specific and include as many -details as necessary, providing background information, and if possible, -suggesting a solution. FBbi editors will be better equipped to address -your suggestions if you offer details regarding *'what is wrong'*, -*'why'*, and *'how to fix it'*. +To help the editorial team to process your request(s), please consider +the following recommendations: -2. **Provide examples and references:** Please include PMIDs/DOIs for -new term requests, and include also screenshots, or URLs illustrating -the current ontology structure for other types of requests. +- **Does the term already exist?** Before submitting a new term request +(NTR), check whether the term you need already exists, either as a +primary term or a synonym term. You can search using an online ontology +browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/fbbi). -3. **For new term request:** Be sure to provide suggestions for label -(name), definition, references, position in hierarchy, etc. +- **Write a detailed request.** A request that simply says “please add a +new term for ‘foo‘” or “please fix the definition of ‘bar’” is unlikely +to be acted upon. Do not assume that the editorial team will know what +“foo” is (or what meaning _you_ give to that term), or what is wrong +with the current definition of “bar”. Please be specific and include as +many details as necessary. + +- **Include suggestions.** You may include suggestions for the precise +label, definition, and optional synonyms that you think the new term you +are requesting should use. If you are familiar with the structure of the +ontology, you may also suggest a position for the new term within the +existing hierarchy. + +- **Provide references.** Whenever possible, please include +PMIDs, DOIs, or other references to source the definition of new or +updated terms. + + +## Contributing to the ontology by editing it directly + +If you know how to edit a OWL ontology, then you may also contribute +more directly by editing it yourself, and submitting your proposed +changes to the editorial team in a pull request (PR). + +If you want to do so, please consider the following recommendations: + +- **Open a ticket prior to submitting a PR.** Even if you plan to make +the changes yourself, you should still start by opening a ticket +explaining what you think the problem is. You may then mention in the +ticket that you plan to fix the issue yourself in an upcoming PR. + +- **Request an ID range.** If you plan to submit PRs in which you will +add new terms, please request (through a dedicated ticket) that an ID +range be assigned to you. + +- **Do not edit fbbi-edit.owl manually.** Please use a specialized +ontology editor such as [Protégé](https://protegeproject.github.io/protege/) +for all your changes. + +If you really want to implement your changes using a non-OWL-aware +program, please make sure to “re-serialize” the `fbbi-edit.owl` file +before committing your changes. + +- **Finding help.** The Biological Imaging Methods Ontology is +maintained using the [Ontology Development Kit](https://github.com/INCATools/ontology-development-kit) +and overall follows (or _attempts_ to follow) the editing guidelines of +the [OBO Foundry](https://obofoundry.org). You can find more +informations about both the ODK and the OBO Foundry practices in the +[OBO Semantic Engineering Training](https://oboacademy.github.io/obook/) +website (commonly known as “the OBOOK”), and you can also find people to +help you in the [OBO Community](obo-communitygroup.slack.com) Slack +workspace. -4. **For updates to relationships:** Provide details of the current -axioms, why you think they are wrong or not sufficient, and what exactly -should be added or removed. On behalf of the Biological imaging methods ontology editorial team, Thanks! diff --git a/README.md b/README.md index cef9bbe..7a78544 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,8 @@ The ontology is known to be used by: * [FlyBase](https://flybase.org/); * [Virtual Fly Brain](https://wwwvirtualflybrain.org/); * the [Cell Image Library](https://www.cellimagelibrary.org/); -* the [Human Cell Atlas](https://www.humancellatlas.org/). +* the [Human Cell Atlas](https://www.humancellatlas.org/); +* the [FoundingGIDE project](https://founding-gide.eurobioimaging.eu). ## Versions diff --git a/src/ontology/fbbi-edit.owl b/src/ontology/fbbi-edit.owl index 930ba00..6e66116 100644 --- a/src/ontology/fbbi-edit.owl +++ b/src/ontology/fbbi-edit.owl @@ -11,6 +11,8 @@ Import() Annotation( ) Annotation( ) Annotation( ) +Annotation( "Chris Woodcock") +Annotation( "Kathy Matthews") Annotation( "This CV covers sample preparation, visualization and imaging methods.") Annotation( ) Annotation( "Biological Imaging Methods Ontology")