Warehouse data (canonical molecules, ontologies) are converted to BioPAX utility classes, such as EntityReference, ControlledVocabulary, EntityFeature sub-classes, and saved as the initial BioPAX model, which forms the foundation for integrating pathway data and for id-mapping.
Pathway and binary interaction data (interactions, participants) are normalized next and merged into the database. Original reference molecules are replaced with the corresponding BioPAX warehouse objects.
The "Pathway Commons" team much appreciates the fundamental contribution of
all the data providers, authors, Identifiers.org,
all the open biological ontologies, the open-source projects and standards,
which made creating of this integrated BioPAX web service and database feasible.