BridgeDb is a framework for finding and mapping equivalent database identifiers. It has many facets: it is both a framework, live services, and are identifier mapping files for genes, proteins, and metabolites.
- The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. BMC Bioinformatics. 2010 Jan 4;11(1):5.
- Scientific lenses to support multiple views over linked chemistry data. Batchelor C, Brenninkmeijer C, Chichester C, Davies M, Digles D, Dunlop I, Evelo CT, Gaulton A, Goble C, Gray AJG, Groth P, Harland L, Karapetyan K, Loizou A, Overington JP, Pettifer S, Steele J, Stevens R, Tkachenko V, Waagmeester A, Williams A, Willighagen EL. In The Semantic Web – ISWC 2014, Lecture Notes in Computer Science Volume 8796, 2014, 98-113.
BridgeDb Framework
- The Application Programming Interface
- The Java Library
BridgeDb Identifier Mapping Databases
- Genes and Proteins (Based on Ensembl & EnsemblGenomes)
- Metabolites (Based on HMDB, ChEBI, and Wikidata)
- Interactions (Based on Rhea)
- Gene-Variant (Ensembl and dbSNP)
BridgeDb plugins to support usage in various environments
- Cytoscape: http://apps.cytoscape.org/
apps/bridgedb - PathVisio: http://www.pathvisio.org/
plugin/bridgedbconfig-plugin/ - R: http://bioconductor.org/packages/devel/bioc/html/BridgeDbR.html (source: https://github.com/BiGCAT-UM/bridgedb-r)
- Bioclipse (under development): https://github.com/egonw/bioclipse.bridgedb
BridgeDb Web Services
BridgeDb mapping functionality is made available via various webservices.
- WikiPathways: REST services
- Open PHACTS: Identifier Mapping Service, Linked Data API
Developer Teams
The following groups (in alphabetical order) are contributing to the development of the BridgeDb world (current or past):
- Gladstone Institutes: Alex Pico, Anders Riutta
- Heriot Watt University: Alasdair Gray
- Maastricht University: Jonathan Mélius, Egon Willighagen, Anwesha Bohler, Martijn van Iersel, Thomas Kelder, Christ Leemans, Denise Slenter, Chris Evelo
- University of Manchester: Christian Brenninkmeijer, Stian Soiland-Reyes, Ian Dunlop, Carole Goble
- Others: Isaac Ho, Jianjiong Gao
Contact
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