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) 2016-09-10

Interaction database
Database Build date
Interactions (all species) 2016-03-23

Gene product/protein database
Database Build date
Homo sapiens 2016-04-14
Mus musulus 2016-04-14
Rattus norvegicus 2016-04-14
Anopheles gambiae 2016-04-14
Arabidopsis thaliana 2016-04-14
Caenorhabditis elegans 2016-04-14
Danio Rerio 2016-04-14
Drosophila melanogaster 2016-04-14
Oryza sativa 2016-04-14
Saccharomyces cerevisiae 2016-04-14
Other species and older versions