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Species are annotated to Rhea reactions, E.C. and other reactions #226

Closed matthiaskoenig closed 7 years ago

matthiaskoenig commented 7 years ago

Species are annotated to Rhea reactions via bqb_is. A species is not a reaction and the reaction does not even have anything to do with the species.

bigg_models v1.3, example e_coli_core.xml

<species boundaryCondition="false" compartment="e" constant="false" fbc:chemicalFormula="HO4P" hasOnlySubstanceUnits="false" id="M_pi_e" metaid="M_pi_e" name="Phosphate" sboTerm="SBO:0000247">
        <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_pi_e">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/pi" />
                  <rdf:li rdf:resource="http://identifiers.org/ncbigi/312945413" />
                  <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00009" />
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM9" />
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00009" />
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/D05467" />
                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00973" />
                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB01429" />
                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB02105" />
                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB02142" />
                  <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB05947" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:14791" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18367" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:26020" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:26078" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:29137" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:29139" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32958" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:39739" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:39745" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:43470" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:43474" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:45024" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:68546" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:68835" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:74873" />
                  <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:7793" />
                  <rdf:li rdf:resource="http://identifiers.org/unipathway.compound/UPC00009" />
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CHORISMATEMUT-RXN" />
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CPD-16459" />
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PHOSPHATE-GROUP" />
                  <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Pi" />
                  <rdf:li rdf:resource="http://identifiers.org/umbbd.compound/c0693" />
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR1159" />
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.99.5" />
                  <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01715" />
                  <rdf:li rdf:resource="http://identifiers.org/rhea/13897" />
                  <rdf:li rdf:resource="http://identifiers.org/rhea/13898" />
                  <rdf:li rdf:resource="http://identifiers.org/rhea/13898" />
                  <rdf:li rdf:resource="http://identifiers.org/rhea/13900" />
                  <rdf:li rdf:resource="http://identifiers.org/unipathway.reaction/UCR01715" />
                  <rdf:li rdf:resource="http://identifiers.org/unipathway.reaction/UER00203" />

http://identifiers.org/rhea/13897 (chorismate <?> prephenate) ?????? http://identifiers.org/rhea/13898 http://identifiers.org/rhea/13898 => also duplicate annotations !!! http://identifiers.org/rhea/13900

Also annotations to other reaction databases which are wrong http://identifiers.org/unipathway.reaction/UCR01715 http://identifiers.org/unipathway.reaction/UER00203 http://identifiers.org/kegg.reaction/R01715

Compound does not have e.c http://identifiers.org/ec-code/5.4.99.5

For me it looks like half of the annotations are wrong. I prefer a very strict limited subset of correct annotations, instead of an overload with annotation of which half are meaningless/incorrect. Not sure if this also happens for other species, but noticed it for phosphate.

matthiaskoenig commented 7 years ago

This seems to be a general problem, i.e. also other species annotated to metanetx reactions.

M_actp_c
http://www.metanetx.org/cgi-bin/mnxweb/equa_info?equa=MNXR82588

and other models, ilT341, M_adphep_LD_c for instance.

Either a general problem with the metanetx database or ModelPolisher. Seems like most species in bigg_models v1.3 are incorrectly annotated to reactions which do not have anything to do with the species.

matthiaskoenig commented 7 years ago

On the other hand reactions are completely under-annotated, i.e. only to BiGG reactions. Even of central enzymes of glycolysis in e_coli_core. Probably all the reaction annotation were written to species !!

matthiaskoenig commented 7 years ago

Just saw that @draeger already found this

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