Development of a use Case for Chemical Resource Description Framework for Acquired Immune Deficiency Syndrome Drug Discovery

The Open Bioinformatics Journal 02 July 2008 RESEARCH ARTICLE DOI: 10.2174/1875036200802010020


There is considerable interest in RDF (Resource Description Framework) as a data representation standard for the growing information technology needs of drug discovery. Though several efforts towards this goal have been reported, most of the reported efforts have focused on text-based data. Structural data of chemicals are a key component of drug discovery and molecular images may offer certain advantages over text-based representations for them. Here we discuss the steps that we used to develop and search chemical Resource Description Framework (RDF) using text and image for structures of relevant to Acquired Immune Deficiency Syndrome (AIDS). These steps are (a) acquisition of the data on drugs, (b) definition of the framework to establish RDF on drugs using commonly asked questions during a drug discovery effort, (c) annotation of the structural data on drugs into RDF using the framework established in step (b), (d) validation of the annotation methods using Semantic Web concepts and tools, (e) design and development of public Web to distribute data to the public, (f) generation and distribution of data using OWL (Web Ontology Language). This paper describes this effort, discusses our observations and announces the availability of the OWL model at the W3C Web site ( The style of this paper is chosen so as to cover a broad audience including structural biologists, medicinal chemists, and information technologists and at times may appear say to the obvious for certain experts. A full discussion of our method and its comparison to other published methods is beyond the scope of this publication.

Keywords: Semantic Web, RDF, Chemical Taxonomy, HIV, AIDS, Structural data, Chemical ontology, Chem-BLAST, Chemical Genomics, Intelligent Web, XML, RDF, OWL, URL: AIDS database and Contact:
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