new blog post: "PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge" https://chem-bla-ics.linkedchemistry.info/2026/01/05/plantmetwiki.html https://doi.org/10.59350/wyz5v-vts33
"I am happy that Elena and Denise pulled me into a collaboration to create an RDF-based knowledge graph about plant pathways."
tl;dr: https://plantmetwiki.bioinformatics.nl/
Replying to this post makes it show up in my blog.
@egonw any way that IRIs like https://identifiers.org/uniprot/Q9SKE0 could be changed to http://purl.uniprot.org/uniprot/Q9SKE0 ? would make federated querying with UniProt so much easier.
@jerven yeah, I know. the second iteration of WikiPathways RDF is long overdue :/
@egonw happy to patch, if I knew where the relevant code is.
@jerven I had not answered your question yet, and no patch needed, but just to answer it:
1. the original (theseus) code is here: https://github.com/wikipathways/GPML2RDF/tree/main which is used for https://sparql.wikipathways.org/
2. the new libGPML-based code is here: https://github.com/egonw/org.pathvisio.io.rdf which is used for https://plantmetwiki.bioinformatics.nl/
@jerven I'm also adding Rhea... anything else from this list that you like to see added? https://bigcat-um.github.io/PRA3006-SPARQL/list.html
Actually, anything from SIB missing in this list?
(well, in terms of EPs... what is missing, is links to SPARQL Examples pages...)
@jerven and SwissLipids RDF IRIs too
@jerven okay, rough estimate of the number of owl:sameAs links now in the @wikipathways RDF (part of the release on the 10th):
- 1250+ owl:sameAs to SwissLipids
- 5000+ owl:sameAs to @lipidmaps.bsky.social
- 1600+ owl:sameAs to @rhea-db.bsky.social
- 77k+ owl:sameAs to UniProtKB
(powered by @wikidata via their SPARQL)
