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SwissLipids Knowledgebase

Linking lipids and lipidomic data with biological knowledge

Description

SwissLipids (www.swisslipids.org) was developed by the Swiss Institute of Bioinformatics (SIB) with the aim to provide a reference resource for lipid biology that supports the integration of lipid and lipidomic data with prior knowledge of lipid structures, metabolic reactions, enzymes, interacting proteins, and functions. SwissLipids is created through a combination of expert curation, bioinformatics, and cheminformatics approaches, in which curated knowledge of lipid metabolic pathways is used to create a library of all lipids structural variants. SwissLipids is tightly linked to bioinformatics resources including the chemical ontology ChEBI (www.ebi.ac.uk/chebi), the Rhea knowledgebase of biochemical reactions (www.rhea-db.org, also based on ChEBI), and UniProtKB/Swiss-Prot (www.uniprot.org).

Technical Information

Export formats:
TSV

Tasks

1) Lipid oriented databases
Searchable by properties:
Name,
Exact mass,
Abbreviation,
Formula,
SMILES,
InChIKey,
ChEBI ID,
LMID ID,
HMDB ID,
Gene names (of associated enzymes),
UniProtKB ID (of associated enzymes)
Calculated physicochemical properties:
NA
Other fields:
Common name,
Systematic name,
Synonyms,
Formula,
Exact mass,
Classification,
Rhea,
UniProt,
PMID
Spectra library:
NA
Structure representations:
2D-image,
InChI,
SMILES
Other identifiers:
ChEBI for all known structures and all components of computationally generated lipids, cross references to LMSD and HMDB, Rhea for reactions, UniProt for proteins, and PMID for citations.
Main identifier:
SLM
Level of annotations:
Structure define level for metabolism and interactions, all levels for location
Has computationally generated lipids:
Yes
Has curated lipids:
Yes
Covered lipid sub classes:
8 out of 8; All lipid categories and classes are included
Structural ontology:
Based on LIPID MAPS® Lipid Classification System and shorthand notation for mass spectrometry. Fully mapped to ChEBI, and hence Rhea and UniProt
Number of lipid structures:
777956