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 and the interaction mappings are obtained from Rhea.


Metabolite database
Database Build date
Metabolites (all species) 2018-05-08

Interaction database
Database Build date
Interactions (all species) 2018-04-25

Gene product/protein database
Database Build date
Homo sapiens 2018-05-09
Mus musulus 2018-05-09
Rattus norvegicus 2018-05-09
Anopheles gambiae 2018-05-09
Arabidopsis thaliana 2018-05-09
Caenorhabditis elegans 2018-05-09
Danio Rerio 2018-05-09
Drosophila melanogaster 2018-05-09
Oryza sativa 2018-05-09
Saccharomyces cerevisiae 2018-05-09
Other species and older versions