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:

Documentation and user guide:

Yes

Download / Web-service link:

Yes

Source code repository:

Yes

Programming languages:

Java,

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: