Structure Database (LMSD)
Introduction | Text/ontology-based search | Structure-based search | Programmatic AccessIntroduction
The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. As of Apr. 21st 2010, LMSD contains 22,500 unique lipid structures, making it the largest public lipid-only database in the world. Structures of lipids in the database come from several sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources; (iv) novel lipids submitted to peer-reviewed journals; (v) computationally generated structures for appropriate glycerolipid and sphingolipid 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 4/21/10)Number of lipids per category
| Fatty acyls | 3562 |
| Glycerolipids | 3036 |
| Glycerophospholipids | 1960 |
| Sphingolipids | 3909 |
| Sterol lipids | 2134 |
| Prenol lipids | 1177 |
| Sacccharolipids | 13 |
| Polyketides | 6709 |
| TOTAL | 22,500 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 [doi:10.1093/nar/gkl838] PMID: 17098933Fahy E, Sud M, Cotter D & Subramaniam S. LIPID MAPS online tools for lipid research Nucleic Acids Research (2007) 35: p. W606-12.PMID:17584797 [doi:10.1093/nar/gkm324] PMID: 17584797
