#57 The SBML file is not valid: weird details

[Binnerman]

Dear all,

when triying to load a sbml file (version 2) y get this messages:

Attribute [cpd00269_c] in 'rxn11955' is unknow
Attribute [cpd15540_c] in 'rxn08231' is unknow
Attribute [cpd15541_c] in 'rxn08232' is unknow
Attribute [cpd15540_c] in 'rxn09106' is unknow
Attribute [cpd15541_c] in 'rxn09107' is unknow
Attribute [cpd000347_c] in 'bio00207' is unknow
Attribute [cpd00659_e] in 'EX_cpd00659_e' is unknow
Attribute [cpd00659_b] in 'EX_cpd00659_e' is unknow
Attribute [cpd00528_e] in 'EX_cpd00528_e' is unknow
Attribute [cpd00528_b] in 'EX_cpd00528_e' is unknow
Attribute [cpd00659_e] in 'rxn01806mod' is unknow
Attribute [p] in 'Seed323098_3' is unknow

But for example for the first error (marked in bold) rxn11955 has cpd00269 metabolite in modelseed database: http://modelseed.org/biochem/reactions/rxn11955

I have attached the file to this issue.

Thanks in advance,
Binnerman

[Anonymous]

Hi Binnerman, sorry for the VERY late reply...

What these errors mean is that the species cpd00269 and the others are not registered in the <listofspecies> section. If you open the SBML file you will see that there is a listOfCompartments, listOfSpecies and listOfReactions. If you want to declare a species (metabolite) as being involved in a reaction (in the listOfReactions section) that species needs first to be declared in the listOfSpecies. </listofspecies>

If you try to validate the file in an online SBML validator you will see that it is not valid. If you exported this from modelSeed, sometimes this happens.

Kind regards