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Models contain annotations to secondary ChEBI metabolites #210

Open matthiaskoenig opened 8 years ago

matthiaskoenig commented 8 years ago

Most of the species contain annotations to the secondary ChEBI metabolites. For instance in model iAB_RBC_283.

<species boundaryCondition="false" constant="false" metaid="M_35cgmp_c" hasOnlySubstanceUnits="false" sboTerm="SBO:0000247" compartment="c" name="3',5'-Cyclic GMP" id="M_35cgmp_c">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:Description rdf:about="#M_35cgmp_c">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/35cgmp" />
                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00697" />
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM665" />
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00942" />
                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB01314" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:11675" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:1327" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:14377" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16356" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:19829" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:39915" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:44955" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:44957" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:57746" />
                  <rdf:li rdf:resource="http://identifiers.org/unipathway.compound/UPC00942" />
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CGMP" />
                  <rdf:li rdf:resource="http://identifiers.org/reactome/30991" />
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </species>

Herin, all the the following chebi annotations are secondary CHEBI:14377, CHEBI:11675, CHEBI:39915, CHEBI:44955, CHEBI:44957, CHEBI:1327, CHEBI:19829 and forward to the primary ChEBI 16356: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16356

see for instance http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:14377

The secondary annotations do not provide any additional information but create problems with many services working with ChEBI identifiers, which most of the time work with the subset of primary annotations. For instance the ontology lookup service OLS cannot retrieve information for secondary ids see http://www.ebi.ac.uk/ols/api/ontologies/CHEBI/terms?obo_id=CHEBI:16356 vs http://www.ebi.ac.uk/ols/api/ontologies/CHEBI/terms?obo_id=CHEBI:14377 which is not resolving.

In my opinion the secondary chebis should be dropped from the model annotations. They

The best Matthias

zakandrewking commented 8 years ago

That makes sense to me.

The source for our CHEBI IDs (http://www.metanetx.org/) does not differentiate primary vs secondary CHEBIs, so we just need to check against CHEBI for each one during loading.

matthiaskoenig commented 5 years ago

Hi all, any progress on this issue? This is very easy to fix. Just check for every chebi id what is the primary chebi id and reduce the annotations to this subset. Best Matthias