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Bioinformatics. 2015 Sep 1;31(17):2860-6. doi: 10.1093/bioinformatics/btv285. Epub 2015 May 5.

The SwissLipids knowledgebase for lipid biology.

Author information

1
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
2
Vital-IT, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.
3
Bioinformatics and Biostatistics Core Facility, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
4
Global Health Institute, École Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland.
5
Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland, Switzerland National Centre of Competence in Research "Chemical Biology", University of Geneva, CH-1211 Geneva, Switzerland and.
6
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland, Vital-IT, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland, Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland, Centre for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.

Abstract

MOTIVATION:

Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide a means to study this complexity, but the interpretation of lipidomic data and its integration with prior knowledge of lipid biology suffers from a lack of appropriate tools to manage the data and extract knowledge from it.

RESULTS:

To facilitate the description and exploration of lipidomic data and its integration with prior biological knowledge, we have developed a knowledge resource for lipids and their biology-SwissLipids. SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures. These are arranged in a hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. SwissLipids provides a reference namespace for lipidomic data publication, data exploration and hypothesis generation. The current version of SwissLipids includes over 244 000 known and theoretically possible lipid structures, over 800 proteins, and curated links to published knowledge from over 620 peer-reviewed publications. We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge.

AVAILABILITY:

SwissLipids is freely available at http://www.swisslipids.org/.

CONTACT:

alan.bridge@isb-sib.ch

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
25943471
PMCID:
PMC4547616
DOI:
10.1093/bioinformatics/btv285
[Indexed for MEDLINE]
Free PMC Article

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