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:

Java

Source code repository:

Yes

Download / Web-service link:

Yes

Documentation and user guide:

Yes

Training datasets:

Publications:

PMID:20047655

Tasks

7.1) Lipid annotations and ID converters

Lipid category coverage:

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