BioPAX uses PSI-MOD (ModificationFeature.modificationType=SequenceModificationVocabulary(PSI-MOD), ModificationFeature.featureLocation) to represent modified proteins. This has several issues
BioPAX can only represent modified proteins; BioPAX cannot represent modified DNA and RNA
PSI-MOD doesn't have concrete definitions of the modified monomers
BioPAX doesn't have attributes to specify linkages
As a result, there's no way to verify that modified proteins describe in BioPAX are valid (i.e. a they specify a unique structure)
Unfortunately, like SBML, there's no straightforward way to integrate BpForms with BioPAX except to embed BpForms in the comments. BioPAX and SBML don't accommodate multiple encodings the way that SBOL does.
Will reach out to developers of BioPAX/PathwayCommons and Reactome. See #38.
jonrkarr
commented
5 years ago
BioPAX uses PSI-MOD (ModificationFeature.modificationType=SequenceModificationVocabulary(PSI-MOD), ModificationFeature.featureLocation) to represent modified proteins. This has several issues
Unfortunately, like SBML, there's no straightforward way to integrate BpForms with BioPAX except to embed BpForms in the comments. BioPAX and SBML don't accommodate multiple encodings the way that SBOL does.
Will reach out to developers of BioPAX/PathwayCommons and Reactome. See #38.