The SwissLipids knowledgebase for lipid biology

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.

Fig. 1.

Browsing SwissLipids. Users can enter the lipid hierarchy at Species level by specifying the desired lipid class and number of carbon atoms and double bonds. The result lists consist of the corresponding Molecular subspecies, Structural subspecies and Isomeric subspecies. Color-coded icons with abbreviations provide an overview of the available information for lipids—their meaning can be revealed by moving the mouse over them. In this example the lipid Species Phosphatidylcholine (O-36:5) has 7 Molecular subspecies, 9 Structural subspecies (for which the list is not expanded) and 20 Isomeric subspecies. The Molecular subspecies Phosphatidylcholine (O-16:0_20:5) and Phosphatidylcholine (O-16:1_20:4) have experimental data on their location in specific tissues or taxa (indicated by the brown “lo” icon), while the Isomeric subspecies 1-O-(1Z-hexadecenyl)-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine has experimental data relating to metabolism (indicated by the purple ‘me’ icon). All lipids have cheminformatic descriptors (green ‘ch’ icon) and are classified (orange ‘cl’ icon) in the SwissLipids hierarchy

Fig. 2.

A SwissLipids entry. SwissLipids entry pages provide information on lipid structure and nomenclature (top panel), cheminformatics descriptors (second panel), lipid classification and components (third panel), reactions (Rhea) and enzymes (UniProtKB) (fourth panel), and subcellular (GO) and tissular (Uberon) location (not shown) which can be navigated through distinct tabs. Links to other databases such as ChEBI, HMDB and LIPID MAPS are also provided. The lipid classification indicates the structural class of lipid (here, 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphocholine) and its ‘analytical parent’ (the Structural subspecies Phosphatidylcholine (P-16:0/20:4)) as well as the individual components (hexadecanol-1-ol and 5Z,8Z,11Z,14Z-eicosatetraenoate) and the annotations available for each. The underlying evidence for curated assertions can be viewed by clicking on ‘see evidence’ (see fourth panel)