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Partially obsoleted term NCBITaxon_1170837 clinocardium californiense #44

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ddooley opened this issue Sep 4, 2020 · 2 comments
Open

Partially obsoleted term NCBITaxon_1170837 clinocardium californiense #44

ddooley opened this issue Sep 4, 2020 · 2 comments

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@ddooley
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ddooley commented Sep 4, 2020

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
@ddooley ddooley changed the title Partially obsoleted term or database snafu? NCBITaxon_1170837 clinocardium californiense Partially obsoleted term NCBITaxon_1170837 clinocardium californiense Sep 4, 2020
allenbaron added a commit to DiseaseOntology/HumanDiseaseOntology that referenced this issue Jul 20, 2023
@allenbaron
Update to latest imports; excludes NCBITaxon
c4869f2 
A number of NCBITaxon terms were removed in the latest release
and need to be reviewed before updating.

The International Committee on Taxonomy of Viruses has renamed a
number of viruses and their taxon IDs have been deprecated but
they were dropped entirely from the OBO version, NCBITaxon. This
is a documented issue that has not been addressed
(obophenotype/ncbitaxon#44).
@cmungall
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cmungall commented Jul 3, 2024

Is the replace-by link in the dmp file?

@jamesaoverton
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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.

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@cmungall @jamesaoverton @ddooley