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) 2017-08-26

Interaction database
Database Build date
Interactions (all species) 2018-01-12

Gene product/protein database
Database Build date
Homo sapiens 2017-11-22
Mus musulus 2017-11-22
Rattus norvegicus 2017-11-22
Anopheles gambiae 2017-11-22
Arabidopsis thaliana 2017-11-22
Caenorhabditis elegans 2017-11-22
Danio Rerio 2017-11-22
Drosophila melanogaster 2017-11-22
Oryza sativa 2017-11-22
Saccharomyces cerevisiae 2017-11-22
Other species and older versions