The identifier mapping that is used in PathVisio is provided by BridgeDb. There are mapping databases available for gene products and metabolites. The gene product databases are created for each species separately.
The metabolite mappings come from HMDB, the gene product mappings are build from Ensembl.
Metabolite database
| Database | Build date |
| Metabolites (all species) | 2011-12-03 |
Gene product/protein database
| Database | Build date |
| Homo sapiens | 2012-06-02 |
| Mus musulus | 2012-06-02 |
| Rattus norvegicus | 2012-06-02 |
| Anopheles gambiae | 2012-06-02 |
| Arabidopsis thaliana | 2012-06-02 |
| Caenorhabditis elegans | 2012-06-02 |
| Danio Rerio | 2012-06-02 |
| Drosophila melanogaster | 2012-06-02 |
| Oryza sativa | 2012-06-02 |
| Saccharomyces cerevisiae | 2012-06-02 |
| Other species and older versions |