Building Chemical Ontology for Semantic Web Using Substructures Created by Chem-BLAST

Efficient and user friendly ontologies are crucial for the effective use of chemical structural data on compounds. This paper describes an automated technique to create a structural ontology for compounds like ligands, co-factors and inhibitors of protein and DNA molecules using a technique developed from Perl scripts, which use a relational database for input and output, called Chem-BLAST (Chemical Block Layered Alignment of Substructure Technique). This technique recursively identifies substructures using rules that operate on the atomic connectivity of compounds. Substructures obtained from the compounds are compared to generate a data model expressed as triples. A chemical ontology of the substructures is made up of numerous interconnected ‘hubs-and-spokes’ is generated in the form of a data tree. This data-tree is used in a Web interface to allow users to zoom into compounds of interest by stepping through the hubs from the top to the bottom of the data-tree. The technique has been applied for (a) 2-D and 3-D structural data for AIDS1; (b) ~60,000 structures from the PDB 2,3. Recently, this technique has been applied to approximately 3,000,000 compounds from PubChem4,5,6. Plausible ways to use this data model for the Semantic Web are also discussed.