+ {%- if prev -%}
+ ← {{ prev.title }}
+ {%- endif -%}
+ {%- if next -%}
+ {{ next.title }} →
+ {%- endif -%}
+
+{%- endif -%}
+
+
+
+
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diff --git a/_includes/toc.html b/_includes/toc.html
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--- /dev/null
+++ b/_includes/toc.html
@@ -0,0 +1,28 @@
+{%- assign html = include.html | default: page.content -%}
+
+{%- comment -%}
+If we were passed Markdown (no + The material for this tutorial is available under + + CC-BY-SA 4.0 International + . + If you have feedback on this documentation, please submit it as a + + GitHub issue + . +
+
+
+
+ 
+
+
+
+
+
\ No newline at end of file
diff --git a/_layouts/docs.html b/_layouts/docs.html
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+++ b/_layouts/docs.html
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+---
+layout: default
+---
+
+{% include topbar.html %}
+
+
+
+
+
+
+
+
+
+
+ {{ content }}
+
+
+
+
diff --git a/_tutorial/1.UnderstandingSPARQL.md b/_tutorial/1.UnderstandingSPARQL.md
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+---
+layout: docs
+title: "Understanding SPARQL Queries"
+order: 10
+---
+
+This page introduces the basic structure of a SPARQL query using a **real example from PlantMetWiki**.
+
+Rather than focusing on abstract syntax, we explain how a concrete biological question is translated into a SPARQL query, and how to interpret each part of the query and its results.
+
+By the end of this page, you should be comfortable:
+
+- reading a SPARQL query used in PlantMetWiki,
+- understanding what biological question it answers,
+- recognizing how pathway content is represented in RDF,
+- following links from PlantMetWiki to external resources such as PlantCyc.
+
+**SPARQL endpoint**:
+https://plantmetwiki.bioinformatics.nl/sparql
+
+**Graph used in all queries**:
+`FROM
+
+
+Question 1: Which part of the query selects the pathway we want to investigate?
+Answer:
+ VALUES ?pathway { <http://rdf-plantmetwiki.bioinformatics.nl/Pathway/RC1000_r20251206224344> }
+
+
+
+Question 2: Which line retrieves all interactions that belong to the pathway?
+Answer:
+ ?pathway gpml:hasInteraction ?interaction .
+
+ Question 3: Why do we filter out
+
+
+
+
diff --git a/_tutorial/2.ExpandQueries.md b/_tutorial/2.ExpandQueries.md
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+---
+layout: docs
+title: "Exploring Species and Pathways"
+order: 20
+---
+
+
+In the previous page, we focused on a **single plant metabolic pathway** and examined how reactions are represented and linked to PlantCyc.
+
+In this section, we take a step back and explore **PlantMetWiki as a collection**:
+- Which plant species are represented?
+- Which pathways exist per species?
+- How can we navigate across species and pathways using SPARQL?
+
+This page introduces **exploratory queries** that help you understand the scope of the database before asking more detailed biological questions.
+
+**SPARQL endpoint**
+https://plantmetwiki.bioinformatics.nl/sparql
+
+**Graph used in all queries**
+```sparql
+FROM Question 3: Why do we filter out _anchor_ interactions?
+ Answer:
+ Interactions that contain _anchor_ are GPML helper nodes used for drawing/connecting edges. They are not real PlantCyc reaction identifiers, so PlantCyc will not recognize them.
+
+
+
+### Which species?
+
+Since we are now retrieving pathways from multiple species, it is useful to explicitly show the species in the results.
+To do this, we modify the SELECT clause so that the organism is visible:
+
+```sparql
+SELECT ?organism ?pathway
+```
+If we also want to include the pathway name (when available), we can extend this further:
+
+```sparql
+SELECT ?organism ?pathway ?pathwayName
+```
+
+And add the corresponding triple pattern:
+```
+OPTIONAL { ?pathway gpml:name ?pathwayName }
+```
+
+### Updated query with pathway names
+```
+PREFIX gpml: How would the VALUES line look if we also want to include Oryza sativa?
+ +Answer:
+
+ VALUES ?organism {
+
+ "Solanum tuberosum"
+ "Arabidopsis thaliana"
+ "Oryza sativa"
+ }
+
+
+
+### Easier querying: discovering species in PlantMetWiki
+
+Unlike Wikidata, PlantMetWiki does not require numeric identifiers (such as Q-numbers).
+Species names are stored directly as literals.
+
+If you are not sure which species are present in the database, you can list them:
+
+```
+PREFIX gpml: Which variable adds the species name to the results?
+Answer:
+ ?organism, filled via ?pathway gpml:organism ?organism
+
+ 
+