
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
License:
Apache-2.0 License
GUI:
Yes
CLI:
Yes
Desktop client:
Yes
Web platform:
Yes
Input formats:
TSV,
CSV,
TXT
Output formats:
Excel,
CSV,
HTML
Platforms:
MacOS,
Linux,
Windows
Programming languages:
R,
Java
Source code repository:
Download / Web-service link:
Documentation and user guide:
Training datasets:
NA
Publications:
PMID:20047655
Tasks
7.1)
Lipid annotations and ID converters
Lipid category coverage:
8
Aspecific
Supported levels of structural annotations:
Lipid and lipid categories (neutral only)
Input annotations or ids:
InChIKey,
InChI,
Isomeric SMILES,
LIPID MAPS ID
Output annotations or ids:
ChemSpider,
PubChem,
ChEBI
Link to the external databases:
HMDB,
ChEBI,
LIPID MAPS LMSD
Other features:
Scientific lenses