As of today, the conversion assumes that physical entities have specific classes associated with them generated automatically as a precondition of building the GO-CAMs. For Reactome this is the REACTO ontology.
For input resources that a) use gene identifiers present in the neo.owl ontology (coming from the GO central GPI file and b) do not use constructs like Sets and c) do not rely heavily on complexes, it would be useful to have the converter make use of the neo IRIs for the physical entity classes.
If the time comes to make this work, look for the currently hard-coded uses of 'GoCAM.reacto_base_iri' in the main BioPax2GO class to get started.
As of today, the conversion assumes that physical entities have specific classes associated with them generated automatically as a precondition of building the GO-CAMs. For Reactome this is the REACTO ontology.
For input resources that a) use gene identifiers present in the neo.owl ontology (coming from the GO central GPI file and b) do not use constructs like Sets and c) do not rely heavily on complexes, it would be useful to have the converter make use of the neo IRIs for the physical entity classes.
If the time comes to make this work, look for the currently hard-coded uses of 'GoCAM.reacto_base_iri' in the main BioPax2GO class to get started.