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MP fails to identify and remove identifiers resources with whitespace-ID #136

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Schmoho opened this issue Dec 1, 2024 · 0 comments
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2.1 Issue in the 2.1 branch bug

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Schmoho commented Dec 1, 2024

Can be observed on model https://www.ebi.ac.uk/biomodels/MODEL2308220001 where this annotation exists:

      <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="-1" fbc:chemicalFormula="C8H12NO6" hasOnlySubstanceUnits="false" id="M_suchms_c" metaid="meta_M_suchms_c" name="O-Succinyl-L-homoserine" sboTerm="SBO:0000247">
        <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="#meta_M_suchms_c">
	<bqbiol:is>
	<rdf:Bag>
[...]
	<rdf:li rdf:resource="https://identifiers.org/chemspider/ "/>
	<rdf:li rdf:resource="https://identifiers.org/hmdb/ "/>
	</rdf:Bag>
	</bqbiol:is>
	</rdf:Description>
          </rdf:RDF>
        </annotation>
            </species>

(chemspider and hmdb annotations)
MP truncates this, so the whitespace is gone.
cobrapy does not recognize the whitespace-ID to be wrong, it does however recognize the version without whitespace to wrong.

The only sane approach I can see here is to delete these annotations.

@Schmoho Schmoho added bug 2.1 Issue in the 2.1 branch labels Dec 1, 2024
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