Functional Group and Substructure Searching as a Tool in Metabolomics

BACKGROUND: A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. METHODOLOGY: We have developed a database named "Biochemical Substructure Search Catalogue" (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. CONCLUSIONS: This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed

Developing Domain Ontologies for Courseware Content

Abstract: Ontologies have the potential to play an important role in educational technology. They can be used to represent knowledge about educational content, supporting instructors in creating content or learners in accessing content in a knowledge-guided way. While ontologies exist for many subject domains, their quality and suitability for the educational context might be unclear. For numerous subjects, ontologies do not exist. We present a method for domain experts rather than ontology engineers to develop ontologies for use in the delivery of courseware content. We will focus in particular on relationship types that allow us to model rich domains adequately. Our investigation will be supported by a case study

Statistics on SUBSTRUCTURE and FGROUP entries in BiSSCat.

<p>Statistics on SUBSTRUCTURE and FGROUP entries in BiSSCat.</p

Partial classification tree of FGROUP: stars indicate FGROUP entries on which no enzymes are known to act.

<p>A complete list of FGROUP entries can be seen at <a href="http://bisscat.org/fgroup.html" target="_blank">http://bisscat.org/fgroup.html</a>.</p

Physicochemical properties defined in SUBSTRUCTURE.

<p>Physicochemical properties defined in SUBSTRUCTURE.</p

Screenshots of BiSSCat website: homepage (top), an example entry of FGROUP (left) and of SUBSTRUCTURE (right).

<p>Screenshots of BiSSCat website: homepage (top), an example entry of FGROUP (left) and of SUBSTRUCTURE (right).</p

IntEnz, the integrated relational enzyme database

IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at http://www.ebi.ac.uk/intenz