How to cite

BridgeDb is a framework for finding and mapping equivalent identifiers from various databases. BridgeDb has many facets: providing a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions. BridgeDb is a 100% Open Science project. The software is available under an Apache License 2.0 and identifier mapping databases under Open licenses, CCZero where possible (e.g. for the metabolite identifier mapping databases). 

When using the framework of BridgeDb, webservice or implementation thereof, please cite:

When discussing the use of BridgeDb to link chemical data or toxicology, please cite:

  • 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.
  • The future of metabolomics in ELIXIR. Van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TM, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O’Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. F1000Research, 6 (2017) .  [version 2; referees: 3 approved]
  • Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials. Martens M,  Verbruggen T, Nymark P, Grafström R, Burgoon LD, Aladjov H, Torres Andón F, Evelo CT, Willighagen EL. Front. Genet. (2018).

When using specific implementation of BridgeDb (related to Cytoscape, and the new mapping files on gene-variants), please cite: