Detection of species identifiers

[jjkoehorst]

A model that I just evaluated contains the following information for a given metabolite:

      <sbml:species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="C_13PDG" name="1,3-Bisphospho-D-glycerate" compartment="c" fbc:chemicalFormula="C3H8O10P2">
        <sbml:annotation>
          <rdf:RDF>
            <rdf:Description rdf:about="#13PDG">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16001"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00236"/>
                  <rdf:li rdf:resource="http://identifiers.org/inchi/InChI=1S/C3H8O10P2/c4-2(1-12-14(6,7)8)3(5)13-15(9,10)11/h2,4H,1H2,(H2,6,7,8)(H2,9,10,11)/t2-/m1/s1"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </sbml:annotation>
      </sbml:species>

This however results 0% chebi / etc.. mapping.

What is happening here?

[ChristianLieven]

Hm that shouldn't happen :S. Could you provide a link to the model or check if the annotation attribute in cobrapy is empty?

I have a suspicion that this error might be on the cobra side, so I'd like to exclude that as a possibility.

I'd be happy to check up on it if the model is accessible.

[jjkoehorst]

The model is currently under review. I will see if I can find a minimalistic model and add this to it to test it further.

[jjkoehorst]

I have added the part to a default memote model. after running memote validation it stays at 0%. Not sure if my example is wrong but if you could check it it would be great! Had to update the first line for prefixes as well.

memote.txt

Line 123 contains the compound info

Update:

Part of SBML file

<sbml:listOfSpecies>
      <sbml:species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_13GLUCAN" name="XXXXXXX1,3-beta-D-GlucanXXXXXXXXXXXXXX" compartment="c" fbc:chemicalFormula="C12H20O10">
        <sbml:annotation>
          <rdf:RDF>
            <rdf:Description rdf:about="#13GLUCAN">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/inchi/InChI=1S/C18H32O16/c19-1-4-7(22)10(25)11(26)17(31-4)34-15-9(24)6(3-21)32-18(13(15)28)33-14-8(23)5(2-20)30-16(29)12(14)27/h4-29H,1-3H2/t4-,5-,6-,7-,8-,9-,10+,11-,12-,13-,14+,15+,16-,17+,18+/m1/s1"/>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:37671"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00965"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </sbml:annotation>
      </sbml:species>

Does indeed not contain annotation information.

[jjkoehorst]

This is the most minimal example I got get which loads but does not show any annotation. Ill have to dive more into cobrapy as it seems that the problem is in there:

<sbml xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">
  <model fbc:strict="true" id="Ecoli_core_model">
    <listOfUnitDefinitions>
      <unitDefinition id="mmol_per_gDW_per_hr">
        <listOfUnits>
          <unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
          <unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
          <unit exponent="-1" kind="second" multiplier="3600" scale="0"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <fbc:listOfObjectives fbc:activeObjective="obj">
      <fbc:objective fbc:id="obj" fbc:type="maximize">
        <fbc:listOfFluxObjectives>
        </fbc:listOfFluxObjectives>
      </fbc:objective>
    </fbc:listOfObjectives>
    <listOfParameters>
      <parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000"/>
      <parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/>
      <parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0"/>
      <parameter constant="true" id="R_ATPM_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="8.39"/>
      <parameter constant="true" id="R_EX_glc_e_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="-10"/>
    </listOfParameters>
    <listOfCompartments>
      <compartment constant="true" id="c" name="Cytoplasm"/>
      <compartment constant="true" id="e" name="Extracellular"/>
    </listOfCompartments>
    <listOfSpecies>
      <species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="C_13PDG" name="1,3-Bisphospho-D-glycerate" compartment="c" fbc:chemicalFormula="C3H8O10P2">
        <annotation>
          <rdf:RDF>
            <rdf:Description rdf:about="#13PDG">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16001"/>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00236"/>
                  <rdf:li rdf:resource="http://identifiers.org/inchi/InChI=1S/C3H8O10P2/c4-2(1-12-14(6,7)8)3(5)13-15(9,10)11/h2,4H,1H2,(H2,6,7,8)(H2,9,10,11)/t2-/m1/s1"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </species>
    </listOfSpecies>
    <fbc:listOfGeneProducts>
    </fbc:listOfGeneProducts>
    <listOfReactions>
    </listOfReactions>
  </model>
</sbml>

[jjkoehorst]

Ok small update, there is something wrong with the header

<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">

Sorry for the many edits but it seems to be related to

fbc:required="false">

Any idea why this is obligatory for annotation?

[Midnighter]

Any SBML-parsing related issues I would re-investigate after https://github.com/opencobra/cobrapy/pull/685 has been merged. I apologize if that's not very satisfying right now but it's the most sane option for us since there are quite a number of known issues with SBML.