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Partially obsoleted term NCBITaxon_1170837 clinocardium californiense #44

Open ddooley opened 4 years ago

ddooley commented 4 years ago

What I see is that NCBI Taxonomy has now

Keenocardium californiense Taxonomy ID: 1421200 (for references in articles please use NCBI:txid1421200) current name Keenocardium californiense (Deshayes, 1839) homotypic synonym:
Cardium californiense Clinocardium californiense

But the NCBITaxon ontology has no labeled reference to http://purl.obolibrary.org/obo/NCBITaxon_1170837 which is presumably Clinocardium californiense. It would be nice to have that entry deprecated and have "term replaced by" pointing to Keenocardium californiense. I see "has alternative id" listing NCBITaxon:1170837 but that used to exist as its own record.

I think there are a number of other examples of this case, e.g. NCBITaxon:110569, NCBITaxon:687680

cmungall commented 3 months ago

Is the replace-by link in the dmp file?

jamesaoverton commented 3 months ago

See https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_readme.txt. There's a merged.dmp file that could probably be used to generate 'replaced by' annotations. I think all other annotations (label, parent, rank, etc.) are just dropped, and would have to be recovered from previous versions.