Make NCBI:txid identifiers secondary ids in the ontology?

[sierra-moxon]

Hello!

It looks like NCBI is using an alternative identifier, ie:

NCBITaxon:7955 (using the taxon ontology)
NCBI:txid7955 (the identifier displayed at NCBI) "Taxonomy ID: 7955 (for references in articles please use NCBI:txid7955)"

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7955&lvl=3&lin=f&keep=1&srchmode=1&unlock

Would it be possible to list the alternative identifier for taxa in the ontology?

[sierra-moxon]

@cmungall - is this doable?

[jamesaoverton]

Someone else asked me this question today. I'm not sure how to answer. Some considerations:

1. It's so trivial to convert "NCBITaxon:7955" to "NCBI:txid7955" that it hardly seems worth the redundant bytes in our OWL file (which is already too big).

2. How are these new "NCBI:txid7995" IDs supposed to resolve? Does the NCBI Taxonomy now provide a resolution service, or term pages with machine-readable content?

3. Should the OBO PURL system provide a way to redirect from http://purl.obolibrary.org/obo/NCBI_txid7955 to existing pages http://purl.obolibrary.org/obo/NCBITaxon_7955? Or somewhere else?

4. Should we take this as an opportunity to harmonize with BioPortal, which provides their own IRIs for NCBI Taxonomy?

I have no answers.

[cmungall]

1 originally I was thinking we could include the xref but I take James point about this being trivial and adding to size of the file.

but maybe we should think about this in the context of mappings for ncbitaxon as a whole. if we have mappings eg to gtdb, should these be bundled in with the owl, or a separate sssom file?

2 This doesn't resolve http://identifiers.org/NCBI:txid7995

neither does http://n2t.net/NCBI/txid7995

3 doesn't seem worth complicating the overall system

4 yes! there is another ticket somewhere...

[balhoff]

Related question: would it be considered courteous if we changed the OBO PURL config to use NCBI for the term browser? E.g., resolve http://purl.obolibrary.org/obo/NCBITaxon_7955 to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7955

Maybe it would even encourage uptake of the PURL.

[jamesaoverton]

One point against that suggestion is that at least Ontobee pages are machine-readable RDF. But I don’t object strongly.

[balhoff]

One point against that suggestion is that at least Ontobee pages are machine-readable RDF. But I don’t object strongly.

I thought about that but I wonder how frequently it's used, especially given that many ontologies currently redirect to specialized browsers (ChEBI, PRO) or OLS. Sorry for hijacking this issue though!