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Gene YCR024C should have uniprot identifier P25345 uniprot identifier not P32903 #372

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oxinabox opened this issue Oct 17, 2024 · 1 comment · Fixed by #375
Closed

Gene YCR024C should have uniprot identifier P25345 uniprot identifier not P32903 #372

oxinabox opened this issue Oct 17, 2024 · 1 comment · Fixed by #375

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@oxinabox
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oxinabox commented Oct 17, 2024

I was going through the model in cobrapy and doing some sensibility checked.
And I noted their were 1161 unique uniprot identifers, but 1162 unique gene ids.
So i went looking closer to see what was going on
and I see that YCR024C and YCR024C-A
are both listed as linked to P32903
And as far as i can tell only the latter ( YCR024C-A) should have that tag
and instead the former (YCR024C) should have P25345, which is not currently present in the model at all.

The relevant section of the SBML is:

<fbc:geneProduct metaid="YCR024C" sboTerm="SBO:0000243" fbc:id="YCR024C" fbc:label="SLM5">
  <annotation>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
      <rdf:Description rdf:about="#YCR024C">
        <bqbiol:is>
          <rdf:Bag>
            <rdf:li rdf:resource="https://identifiers.org/uniprot/P32903"/>
          </rdf:Bag>
        </bqbiol:is>
      </rdf:Description>
    </rdf:RDF>
  </annotation>
</fbc:geneProduct>
<fbc:geneProduct metaid="YCR024C__45__A" sboTerm="SBO:0000243" fbc:id="YCR024C__45__A" fbc:label="PMP1">
  <annotation>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
      <rdf:Description rdf:about="#YCR024C__45__A">
        <bqbiol:is>
          <rdf:Bag>
            <rdf:li rdf:resource="https://identifiers.org/uniprot/P32903"/>
          </rdf:Bag>
        </bqbiol:is>
      </rdf:Description>
    </rdf:RDF>
  </annotation>
</fbc:geneProduct>
@edkerk
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edkerk commented Oct 17, 2024

Will get this fixed. For sanity, we'll check all UniProt IDs.

@edkerk edkerk mentioned this issue Nov 23, 2024
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2 participants