LMSD text search tutorial

Introduction

The LMSD Text/Ontology search may be used to search the LIPID MAPS structure database (LMSD) by lipid classification, common name, systematic name or synonym, LIPID MAPS ID, lipid mass (neutral form), lipid formula or ontology parameter. The user may select multiple criteria in order to perform an "AND" search. Data for the number of carbons (number of side-chain carbons in the case of GL,GP and SP entries containing acyl/alkyl chains), number of double/triple bonds, number of rings and number of a wide variety of functional groups has been obtained for each lipid entry, and this enables users to specify up to 4 criteria in the 'Ontology search parameters' section of the search.


Example: Searching by a combination of partial name and classification term

The user selects 'Fatty acyls' as the lipid category and 'Fatty acids and conjugates' as the main class. The partial name 'lin' is specified in the 'Name' field. The results page returns all lipids in the 'Fatty acids and conjugates' main class which contain the substring 'lin' in either their common name, systematic name or synonym(s), for example, linoleic acid.


Example: Searching by a combination of mass, classification term and lipid ontology terms

The user selects 'Fatty acyls' as the lipid category and 'Eicosanoids' as the main class and 'Prostaglandins' as the sub-class. A mass of 352 is specified in the 'Mass' field. Ontology parameters are chosen to specify exactly 2 double bonds and 1 oxo (keto) group. In this particular case, all lipids classified as Prostaglandins with a neutral mass within 0.5 daltons of 352 and which contain 2 double bonds and 1 oxo (keto) group will be returned.

logo LIPID MAPS® is funded by a grant from the Wellcome Trust.