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BiGCAT-UM / KinRDF

Conversion of kinetic data to an RDF model, compatible with WikiPathways PathWayModels
MIT License
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PubMed prefix #7

Closed DeniseSl22 closed 1 year ago

DeniseSl22 commented 1 year ago

@egonw, a question:

WPRDF currently uses the following prefix for Pubmed:

@prefix pubmed:   <http://www.ncbi.nlm.nih.gov/pubmed/> .

While I now use:

@prefix PMID:   <http://identifiers.org/pubmed/> .

Any thought, suggestions, on which option is best? I don't mind aligning to WP (maybe also keeping the redirects on the WPmain PW pages working), but for other resources, we do use identifiers.org.

I also found this paper on NCBI SPARQL, and wanted to check the PMID prefix in there, however the SPARQL endpoint doesn't seem to be available (I found a Biostart question from you on this from ~11 years ago,the URLs don't work anymore).

DeniseSl22 commented 1 year ago

The BridgeDb Datasources repo shows that the ncbi.nlm.nih.gov is the link used in WP linkouts (but with httpS, so we might need to update the WPRDF code for this as well): image

egonw commented 1 year ago

The datasources.tvs does not really have IRI patterns, just website URL patterns.

IRI compatibility was one of the themes of that meeting yesterday evening.

DeniseSl22 commented 1 year ago

https://github.com/BiGCAT-UM/KinRDF/commit/287b3679afd4e9da03e6310d2e8858aefe136453