Frequently asked questions

Frequently asked questions and troubleshooting tips.

General questions

Q: Do you guarantee the API stability?

Yes, see the ApiStability note.

Q: How do I cite BridgeDb in a scientific publication?

Please cite

van Iersel, M.P. et al. (2010) The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services BMC Bioinformatics 11:5  full text

Mapping questions

Q: Does BridgeDb support many-to-many mappings?

Yes, many-to-many mappings are supported at the API level: the mapId(Xref) method returns a Set, and the mapId(Set<Xref>) method returns a Map<Xref, Set<Xref>> to support multiple targets per source identifier.

The batchmapper tool supports many-to-many mappings using the recently added -mm switch.

Troubleshooting questions

Q: I get "idmapper-pgdb" protocol not found (or similar)

The appropriate driver has to register itself first. To do so, call Class.forName("....") where you fill in the appropriate driver class. See MappingServicesInfo for a list of protocols and their corresponding driver classes.

Q: I get NullPointerException when using the BridgeRest driver

Make sure you call BioDataSources.init(); before using the driver. If that doesn't help, you've found a bug! Please send us a bug report.

Q: I get ClassNotFoundException with the idmapper-pgdb protocol.

Make sure you include derby.jar in the classpath.