The LIPID MAPS Structure Database (LMSD) is a relational database that contains structures and annotations of biologically relevant lipids. Lipid structures in LMSD are sourced from four main areas: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; and (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, and other public sources. All lipid structures in LMSD are drawn in a consistent manner based on a defined drawing scheme. Users can search LMSD using either text-based or structure-based search options. The text-based search supports data retrieval by any combination of data fields such as LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass. The structure-based search allows for substructure or exact match searches. Search results include structure, annotations, and links to external databases. LMSD is publicly available at www.lipidmaps.org/data/structure/. LMSD uses a comprehensive classification system for lipids, dividing them into eight categories. Each category is further divided into classes and subclasses. A consistent nomenclature scheme has also been developed to provide systematic names for various classes and subclasses of lipids. All lipids in LMSD are classified and annotated using this system. Lipid structures in LMSD are drawn according to a consistent framework proposed by the LIPID MAPS consortium. Structures of all lipids in LMSD adhere to the structure drawing rules proposed by the LIPID MAPS consortium. LMSD is implemented as a relational database using Oracle9i Enterprise Edition. It provides a relational database with a graphical user interface (GUI) for querying and browsing. LMSD supports both text-based and structure-based searches. The database also includes a unique 12-character LIPID MAPS identifier (LM ID) for each lipid structure. LMSD also maintains links to PubChem substance ID (SID) and provides access to complete sets of lipid structures. LMSD is a growing database of lipids, with data from existing databases and scientific literature added regularly. It is also used to store novel lipids identified and characterized by the LIPID MAPS core laboratories. As of November 2006, LMSD contains 9143 lipids. Future work involves tighter integration and cross-referencing of lipids in LMSD with lipid-associated proteins and genes in the LIPID MAPS proteome database (LMPD).The LIPID MAPS Structure Database (LMSD) is a relational database that contains structures and annotations of biologically relevant lipids. Lipid structures in LMSD are sourced from four main areas: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; and (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, and other public sources. All lipid structures in LMSD are drawn in a consistent manner based on a defined drawing scheme. Users can search LMSD using either text-based or structure-based search options. The text-based search supports data retrieval by any combination of data fields such as LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass. The structure-based search allows for substructure or exact match searches. Search results include structure, annotations, and links to external databases. LMSD is publicly available at www.lipidmaps.org/data/structure/. LMSD uses a comprehensive classification system for lipids, dividing them into eight categories. Each category is further divided into classes and subclasses. A consistent nomenclature scheme has also been developed to provide systematic names for various classes and subclasses of lipids. All lipids in LMSD are classified and annotated using this system. Lipid structures in LMSD are drawn according to a consistent framework proposed by the LIPID MAPS consortium. Structures of all lipids in LMSD adhere to the structure drawing rules proposed by the LIPID MAPS consortium. LMSD is implemented as a relational database using Oracle9i Enterprise Edition. It provides a relational database with a graphical user interface (GUI) for querying and browsing. LMSD supports both text-based and structure-based searches. The database also includes a unique 12-character LIPID MAPS identifier (LM ID) for each lipid structure. LMSD also maintains links to PubChem substance ID (SID) and provides access to complete sets of lipid structures. LMSD is a growing database of lipids, with data from existing databases and scientific literature added regularly. It is also used to store novel lipids identified and characterized by the LIPID MAPS core laboratories. As of November 2006, LMSD contains 9143 lipids. Future work involves tighter integration and cross-referencing of lipids in LMSD with lipid-associated proteins and genes in the LIPID MAPS proteome database (LMPD).