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The BiGG Models website server
http://bigg.ucsd.edu
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Annotating models with the genome identifier #368

Open Midnighter opened 4 years ago

Midnighter commented 4 years ago

Many models in BiGG are currently annotated with a taxonomic identifier and a reference to the model itself, for example, as shown below.

    <annotation>
      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
        <rdf:Description rdf:about="#iML1515">
          <bqbiol:hasTaxon>
            <rdf:Bag>
              <rdf:li rdf:resource="http://identifiers.org/taxonomy/511145" />
            </rdf:Bag>
          </bqbiol:hasTaxon>
          <bqmodel:is>
            <rdf:Bag>
              <rdf:li rdf:resource="http://identifiers.org/bigg.model/iML1515" />
            </rdf:Bag>
          </bqmodel:is>
        </rdf:Description>
      </rdf:RDF>
    </annotation>

On the website, BiGG also provides a link to the genome sequence that was used to create the model, see, for example, http://bigg.ucsd.edu/models/iML1515.

Where possible, it would be great to also create MIRIAM compliant annotations of the genome on the model using the identifier from the genome database or RefSeq namespaces as defined at Identifiers.org. Or maybe this is a task for ModelPolisher @draeger ?

draeger commented 4 years ago

@Midnighter, yes, this is indeed something ModelPolisher could do. I am creating an issue there for this topic.