how to represent post translational modifications

[goodb]

Reactome has entities like p-2T-MAP2K1 that are combinations of proteins with different modifications. For p-2T-MAP2K1 it is actually a set of two proteins with the same id (UniProt:Q02750) but with different PTMs.

Currently the GO-CAM view of this entity is a single instance of a UniProt:Q02750 without any PTM information. This leads to representations of function/reaction nodes that have the same entities as both input and output (apart from ATP->ADP).

Is this a desirable representation for GO-CAM models?

Note that the BioPAX export does contain information about the specific sequence locations that are modified. In principal, this information could be captured in the GO-CAM model.

[goodb]

Noting here that I have currently adopted the pattern applied by PRO for capturing modifications in the reactome entity ontology (reo). PRO and REO consider modified forms of proteins subclasses of the canonical protein, distinguished by the addition of subclass_of (has_part modification class) axioms. Modification classes come from the protein modification ontology http://purl.obolibrary.org/obo/mod.owl .

[goodb]

Conversion to use of reactome entities closes this issue (in the context of the go-cams). May re-emerge during specific export processes but those will be new issues.