wikipathways / wikipathways/GPML2RDF

add Bioregistry-style compact identifiers

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#117 2 comments 0 reactions 1 assignee View on GitHub

@egonw is already working on this.

Since Jun 11, 2023.

enhancement question
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Description

@cthoyt, let's say, I would be adding Bioregistry-style compact identifiers as Literals to the WikiPathways RDF, is there already an ontology with a predicate for such identifiers?

Let's say we have this:

<https://identifiers.org/ensembl/ENSG00000139163>
        rdf:type            wp:GeneProduct , wp:DataNode ;
        rdfs:label          "ETNK1" ;
        wp:bdbEnsembl       <https://identifiers.org/ensembl/ENSG00000139163> ;
        wp:bdbEntrezGene    <https://identifiers.org/ncbigene/55500> ;
        wp:bdbHgncSymbol    <https://identifiers.org/hgnc.symbol/ETNK1> ;
        wp:bdbUniprot       <https://identifiers.org/uniprot/A0A5K1VW28> , <https://identifiers.org/uniprot/Q86U68> , <https://identifiers.org/uniprot/Q9HBU6> , <https://identifiers.org/uniprot/H0YH69> , <https://identifiers.org/uniprot/H0YFP7> , <https://identifiers.org/uniprot/A0A
5F9ZI33> ;
        wp:bdbWikidata      <http://www.wikidata.org/entity/Q18041828> .

And I would add something like x:y as below, what should x:y be (ps, ignore the prefixes, I didn't check them; you get the point)?

<https://identifiers.org/ensembl/ENSG00000139163>
        x:y       "ensembl:ENSG00000139163" , ncbigene:55500", "hgnc.symbol:ETNK1", uniprot:A0A5K1VW28", "uniprot:Q9HBU6", "uniprot:H0YH69", "uniprot:H0YFP7", "uniprot/A0A5F9ZI33, "wikidata:Q18041828" ;

I could use wp:bdbBioregistry but maybe you have something better in mind?

(yes, once we're done with full RDF support in Bioregistry we can add that too)

cc @DeniseSl22 @marvinm2 @ammar257ammar

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