BridgeDb and Wikidata: a powerful combination generating interoperable open research (BridgeDb)

Abstract

Like humans have a unique social security number and different phone numbers from various providers, so do proteins and metabolites have a unique structure but different identifiers from various databases. BridgeDb is an interoperability platform that allows combining these databases, by matching database-specific identifiers. These matches are called identifier mappings, and they are indispensable when combining experimental (omics) data with knowledge in reference databases. BridgeDb takes care of this interoperability between gene, protein, metabolite, and other databases, thus enabling seamless integration of many knowledge bases and wet-lab results. Since databases get updated continuously, so should the Open Science BridgeDb project.

MSMetaEnhancer: A Python package for mass spectra metadata annotation

“…Similarly, RaMP cross-references multiple database specific identifiers via their internal RaMP_ID to integrate various pathway and compound databases (Zhang et al, 2018). BridgeDb is an ELIXIR project providing mapping functionality of different identifiers present in HMDB (e.g., PubChemCID, ChEBI and InChIKey), gene information and several pathway databases in an organism centric manner, exposing a Java and REST API (van Iersel et al, 2010;Willighagen et al, 2022).…”