Some confusion about the URL to be used for NCBIGene in the prefix map

[gaurav]

The NCBIGene concept IRI prefix in the Biolink Model prefix map is http://identifiers.org/ncbigene/:

https://github.com/biolink/biolink-model/blob/ce4f70988e4141b50fe9e1161d696483094fe192/prefix-map/biolink-model-prefix-map.json#L121

However, Ubergraph thinks the concept IRI prefix should actually be https://identifiers.org/ncbigene/ (i.e. https instead of http), which comes from the Provisional Cell Ontology (PCL), while identifiers.org thinks it should be https://identifiers.org/ncbigene: or https://www.ncbi.nlm.nih.gov/gene/ (https://registry.identifiers.org/registry/ncbigene).

I would propose that Biolink Model goes with https://identifiers.org/ncbigene/ to keep us in sync with Ubergraph, but I don't know if these identifier.org concept need to be rethought at some point.

@balhoff Any thoughts on this?

[balhoff]

Ubergraph just has what comes from the source ontologies, so I think the thing to do here is try to convince PCL that they should be using http instead of https for identifiers. We (@sierra-moxon really) made some changes like this to align things in GO-CAM recently.

[cmungall]

Yes, in fact identifiers.org has over the years given 2x2 options (http vs https, slash vs hash). From a web browser POV it doesn't matter, they all resolve. But for semantic URIs this indecision destroys interoperability between triplestores.

as http-with-slash was the first that is what many groups adopted first, so we should stick to that. If we do make a change it should be something with absolute guaranteed cast iron permanence.

[sierra-moxon]

I followed up with the CL folks, and they had just had a new release with this change merged in. I am going to call this Biolink issue closed as I imagine @balhoff's ubergraph will be updated automatically, and that will trigger a fix for you, @gaurav -- please of course reopen if I missed a component.