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Remove extra # symbol from IRIs of some taxonomic rank terms? #96

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allenbaron opened this issue Jan 25, 2024 · 2 comments · May be fixed by #120
Open

Remove extra # symbol from IRIs of some taxonomic rank terms? #96

allenbaron opened this issue Jan 25, 2024 · 2 comments · May be fixed by #120

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@allenbaron
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Three taxonomic rank terms appear to have an extra # in their IRIs:

  1. http://purl.obolibrary.org/obo/NCBITaxon#_species_group
  2. http://purl.obolibrary.org/obo/NCBITaxon#_species_subgroup
  3. http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank

All other taxonomic rank IRIs use the prefix http://purl.obolibrary.org/obo/NCBITaxon_.

Should the extra # be removed from these IRIs?

Noting that none of the taxonomic rank terms have IRIs that resolve.

@balhoff
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balhoff commented Jan 25, 2024

Should NCBITaxon use identifiers from the OBO TAXRANK ontology?

@cmungall
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taxrank is probably a bigger decision, but I think it makes sense. Made a distinct issue #97

The odd URI issue is an unfortunate but known consequence of

  • how we decided to model the URIs for the subsets
  • how these are translated into obo format

It was probably a mistake for us to place the subsets directly in the NCBITaxon namespace, we don't own this. Should have been done the same way as go/uberon/doid/etc, which is suboptimal but predictable.

The decision is

  1. leave as is for now and make a bigger change to taxrank (Switch to taxrank for ranks, and decide on the metamodel #97) later
  2. change the namespace for the subset to be obo:ncbitaxon# (fixing the weirdness issue)

@cthoyt cthoyt linked a pull request Nov 27, 2024 that will close this issue
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3 participants