The identifier mapping that is used in PathVisio is provided by BridgeDb. There are mapping databases available for gene products, metabolites and interactions. The gene product databases are created for each species separately.

The metabolite mappings come from HMDB, ChEBI, and Wikidata, the gene product mappings are build from Ensembl, the interaction mappings are obtained from Rhea.


Metabolite database
Database Latest Build date (also supported by BridgeDb API)
Metabolites (all species) 2019-02-07

Interaction database
Database Latest build date
Interactions (all species) 2019-05-22

Gene product/protein database (Ensembl 91).
Database Latest Build date (also supported by BridgeDb API)
GeneProtein (various species) 2018-05-09