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Lipid Classification System

Posted in Biochemical pathways, Cell Biology, Curation, Fatty acids, Lipid metabolism, Lipids, Metabolism, Metabolomics, Signaling & Cell Circuits, tagged , , , , on October 26, 2014| Leave a Comment »

Lipid Classification System

Curator: Larry H. Bernstein, MD, FCAP

Lipid Classification, Nomenclature and Structure Drawing

 

The LIPID MAPS consortium has developed a comprehensive classification, nomenclature, and chemical representation system for lipids, the details of which are described in the May 2009 issue of the Journal of Lipid Research:

Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T, Spener F, van Meer G, Wakelam M and Dennis E.A.,Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. (2009) 50: S9-S14.PubMed ID:19098281.

Fahy E, Subramaniam S, Brown H, Glass C, Merrill JA, Murphy R, Raetz C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, Vannieuwenhze M, White S, Witztum J and Dennis E.A.,A comprehensive classification system for lipids. J. Lipid Res. (2005) 46: 839-861.PubMed ID:15722563.

http://www.lipidmaps.org/resources/tutorials/lipid_cns.html

Lipid Classification System

The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own sublassification hierarchy.

All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID’s (LM_ID) which reflects their position in the classification hierarchy.

LMSD can be searched by lipid class, common name, systematic name or synonym, mass, InChIKey or LIPID MAPS ID with the “Quick Search” tool on the home page, or alternatively, by

LIPID MAPS ID, systematic or common name, mass, formula, category, main class, subclass data, or structure or sub-structure with one of the search interfaces in the LMSD database section.

Each LMSD record contains an image of the

  • molecular structure,
  • common and systematic names,
  • links to external databases,
  • Wikipedia pages (where available),
  • other annotations and links to structure viewing tools.

In addition to LMSD search interfaces, you can drill down through the classification hierarchy below to the LMSD record for an individual lipid.

 

Lipid Classes
Fatty Acyls [FA] Fatty Acids and Conjugates [FA01]Octadecanoids [FA02]Eicosanoids [FA03]

Docosanoids [FA04]

Fatty alcohols [FA05]

Fatty aldehydes [FA06]

Fatty esters [FA07]

Fatty amides [FA08]

Fatty nitriles [FA09]

Fatty ethers [FA10]

Hydrocarbons [FA11]

Oxygenated hydrocarbons [FA12]

Fatty acyl glycosides [FA13]

Other Fatty Acyls [FA00]

 Glycerophospholipids [GP] Glycerophosphocholines [GP01]Glycerophosphoethanolamines [GP02]Glycerophosphoserines [GP03]

Glycerophosphoglycerols [GP04]

Glycerophosphoglycerophosphates [GP05]

Glycerophosphoinositols [GP06]

Glycerophosphoinositol monophosphates [GP07]

Glycerophosphoinositol bisphosphates [GP08]

Glycerophosphoinositol trisphosphates [GP09]

Glycerophosphates [GP10]

Glyceropyrophosphates [GP11]

Glycerophosphoglycerophosphoglycerols [GP12]

CDP-Glycerols [GP13]

Glycosylglycerophospholipids [GP14]

Glycerophosphoinositolglycans [GP15]

Glycerophosphonocholines [GP16]

Glycerophosphonoethanolamines [GP17]

Di-glycerol tetraether phospholipids (caldarchaeols) [GP18]

Glycerol-nonitol tetraether phospholipids [GP19]

Oxidized glycerophospholipids [GP20]

Other Glycerophospholipids [GP00]
Glycerolipids [GL] Monoradylglycerols [GL01]Diradylglycerols [GL02]Triradylglycerols [GL03]

Glycosylmonoradylglycerols [GL04]

Glycosyldiradylglycerols [GL05]

Other Glycerolipids [GL00]

 Sphingolipids [SP] Sphingoidbases [SP01]Ceramides [SP02]Phosphosphingolipids [SP03]

Phosphonosphingolipids [SP04]

Neutral glycosphingolipids [SP05]

Acidic glycosphingolipids [SP06]

Basic glycosphingolipids [SP07]

Amphoteric glycosphingolipids [SP08]

Arsenosphingolipids [SP09]

Other Sphingolipids [SP00]
Sterol Lipids [ST] Sterols [ST01]Steroids [ST02]Secosteroids [ST03]

Bile acids and derivatives [ST04]

Steroid conjugates [ST05]

Other Sterol lipids [ST00]

 Prenol Lipids [PR] Isoprenoids [PR01]Quinones andhydroquinones [PR02]Polyprenols [PR03]

Hopanoids [PR04]

Other Prenol lipids [PR00]
Saccharolipids [SL] Acylaminosugars [SL01]Acylaminosugarglycans [SL02]Acyltrehaloses [SL03]

Acyltrehalose glycans [SL04]

Other acyl sugars [SL05]

Other Saccharolipids [SL00]

 Polyketides [PK] Linearpolyketides [PK01]Halogenatedacetogenins [PK02]Annonaceae acetogenins [PK03]

Macrolides and lactone polyketides [PK04]

Ansamycins and related polyketides [PK05]

Polyenes [PK06]

Linear tetracyclines [PK07]

Angucyclines [PK08]

Polyether polyketides [PK09]

Aflatoxins and related substances [PK10]

Cytochalasins [PK11]

Flavonoids [PK12]

Aromatic polyketides [PK13]

Non-ribosomal peptide/polyketide hybrids [PK14]

Other Polyketides [PK00]

 

 

LIPID MAPS Structure Database (LMSD)

 

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. As of May 3, 2013, LMSD contains over 37,500 unique lipid structures, making it the largest public lipid-only database in the world. Structures of lipids in the database come from several sources:

  • LIPID MAPS Consortium’s core laboratories and partners;
  • lipids identified by LIPID MAPS experiments;
  • biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources;
  • novel lipids submitted to peer-reviewed journals;
  • computationally generated structures for appropriate classes.

All the lipid structures in LMSD adhere to the structure drawing rules proposed by the LIPID MAPS consortium. A number of structure viewing options are offered: gif image (default), Chemdraw (requires Chemdraw ActiveX/Plugin), MarvinView (Java applet) and JMol (Java applet).

All lipids in the LMSD have been classified using the LIPID MAPS Lipid Classification System. Each lipid structure has been assigned a LIPID MAPS ID (LM_ID) which reflects its position in the classification hierarchy. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options.

 

The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases.

Statistics

(as of 10/8/14)

Number of lipids per category

Fatty acyls          5869

Glycerolipids       7541

Glycerophospholipids       8002

Sphingolipids      4338

Sterol lipids         2715

Prenol lipids        1259

Sacccharolipids  1293

Polyketides         6742

TOTAL  37,759 structures

References

Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S. LMSD: LIPID MAPS structure database Nucleic Acids Research 35: p. D527-32. PMID:17098933 [http://dx.doi.org:/10.1093/nar/gkl838]     PMID: 17098933

Fahy E, Sud M, Cotter D & Subramaniam S. LIPID MAPS online tools for lipid research Nucleic Acids Research (2007) 35: p. W606-12.PMID:17584797 [http://dx.doi.org:/10.1093/nar/gkm324] PMID: 17584797

 

Proteome Database (LMPD)

– over 2,400 lipid-associated proteins from human and mouse

Pathways

– manually curated lipid metabolism and signaling pathways

MS analysis tools

– tools for searching various lipid classes by precursor or product ion

Structure Drawing Tools

– draw and save lipid structures using online menus

 

References

Time-varying causal inference from phosphoproteomic measurements in macrophage cells.

IEEE Trans Biomed Circuits Syst. 2014 Feb;8(1):74-86.
http://dx.doi.org:/10.1109/TBCAS.2013.2880235.

 

 

research highlights icon Modeling of eicosanoid fluxes reveals functional coupling between cyclooxygenases and terminal synthases.

Biophys J. 2014 Feb 18;106(4):966-75.
http://dx.doi.org:/10.1016/j.bpj.2014.01.015.

 

Lipid Classification

Starting from a lipid category, the user can navigate through the hierarchy by clicking on the “[+]” icon next to a main class name.

This will expand that item to reveal its sub classes.

Clicking on hyperlinks to the right of main classes, sub classes or level 4 classes will display a tabular listing of all lipids corresponding to that particular subset in the LMSD database.

Finally, clicking on the LM_ID hyperlink displays the LMSD record for an individual lipid, which contains

  • an image of the molecular structure,
  • common and systematic names,
  • links to external databases,
  • Wikipedia pages (where available),
  • other annotations and links to structure viewing tools.

LIPID MAPS classification hierarchy

Category (Example: Prenol lipids [LMPR])

Main class (Example: Isoprenoids [LMPR01])

Sub class (where applicable) (Example: C15 Isoprenoids (sesquiterpenes) [LMPR0103])

Level 4 class (where applicable) (Example: Bisabolane sesquiterpenoids [LMPR010306])

Pathways

We have carefully constructed these lipid pathways based on LIPID MAPS experimental data and data from the literature. LIPID MAPS experimental data obtained from our lipid time course experiments and microarray experiments on macrophagese were mapped to corresponding lipids and genes, respectively.

Pathway maps created using VANTED

VANTED is a tool for the visualization and analysis of networks with related experimental data. For more information on VANTED, please refer to: Björn H. Junker, Christian Klukas and Falk Schreiber (2006): VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7:109 (http://www.biomedcentral.com/1471-2105/7/109)

References

Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T, Spener F, van Meer G, Wakelam M and Dennis E.A.,Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. (2009) 50: S9-S14.PubMed ID:19098281.

Fahy E, Subramaniam S, Brown H, Glass C, Merrill JA, Murphy R, Raetz C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, Vannieuwenhze M, White S, Witztum J and Dennis E.A.,A comprehensive classification system for lipids. J. Lipid Res. (2005) 46: 839-861.PubMed ID:15722563.

Introduction to lipids

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