BridgeDb logo

BridgeDb

(Lipid) Identifier mapping

Description

BridgeDb is a set of identifier mapping tools, which allows mapping an identifier from one database to identifier from one or more other databases. BridgeDb provides a Java library, a webservice, and multiple identifier mapping databases. The latter databases come from trusted sources, and can be created for specific sources too. BridgeDb has been selected as an ELIXIR Recommended Interoperability Resource and has been used by projects like WikiPathways and Open PHACTS. For lipid identifiers, BridgeDb relies on Wikidata, which maps identifiers based on InChIKey identification, to e.g. LIPID MAPS, ChEBI. HMDB, and research literature. Protein and Gene identifiers are also available.

Technical Information

Publications:
PMID:20047655
Training datasets:
NA
Download / Web-service link:
Source code repository:
Programming languages:
Java,
R
Platforms:
Windows,
Linux,
MacOS
Output formats:
HTML,
CSV,
Excel
Input formats:
TXT,
CSV,
TSV
Web platform:
Yes
Desktop client:
Yes
CLI:
Yes
GUI:
Yes
License:
Apache-2.0 License

Tasks

7.1) Lipid annotations and ID converters
Other features:
Scientific lenses
Link to the external databases:
LIPID MAPS LMSD,
ChEBI,
HMDB
Output annotations or ids:
ChEBI,
PubChem,
ChemSpider
Input annotations or ids:
LIPID MAPS ID,
Isomeric SMILES,
InChI,
InChIKey
Supported levels of structural annotations:
Lipid and lipid categories (neutral only)
Lipid category coverage:
8