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Dev - #8

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elenadelpup merged 9 commits into
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Jul 3, 2026
Merged

Dev#8
elenadelpup merged 9 commits into
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dev

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All 5 tutorial pages updated to use the current PlantMetWiki RDF structure:

- Replace FROM <old-default-graph> with named GRAPH blocks
- Replace gpml:hasInteraction / gpml:hasDataNode (don't exist) with dcterms:isPartOf
- Replace gpml:organism "string" on pathway (returns only Viridiplantae) with
  proper 3-graph species join: gpml-taxonomy-extra + ncbitaxon label lookup
- Fix BGC queries: BGC data is in graph/bgc-plantismash and graph/bgc-mibig,
  joined to pathways via shared identifiers.org gene IRIs (not wp:participants)
- Fix Capsicum.md: dc:identifier pmw:PC629 -> FILTER on pathway IRI;
  species pattern updated; added reaction-coverage-by-species query
- Switch federated queries from Qlever (rate-limited) to query.wikidata.org
- Reaction IDs extracted from IRI tail (no dc:identifier on wp:Conversion)
@elenadelpup
elenadelpup merged commit 13ec740 into master Jul 3, 2026
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