Abstract
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 (http://esw.w3.org/topic/HCLS/ChemicalTaxonomiesUseCase). 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.
Highlights
The size of chemical databases has grown exponentially in recent years and there is an urgent need for novel data representation techniques and user-friendly search engines that enable the effective use of these data resources
We discuss our efforts towards this goal in the context of the structural data represented either as text-based or imagebased data and distributed by an Acquired Immune Deficiency Syndrome (AIDS) structural database
Some of the important aspects in the development of this information model with emphasis on drug design are as follows. a) Develop a rule based on a dictionary of fragments and linkers that may have specific semantics from the view point of structure-based drug discovery. b) Use this dictionary to develop all individual entities, class, class axioms relevant to the use case. c) Extend the dictionary, entities, OWL Class and OWL Class axioms to cover all compounds of interest for the use case
Summary
The size of chemical databases has grown exponentially in recent years and there is an urgent need for novel data representation techniques and user-friendly search engines that enable the effective use of these data resources. The Semantic Web is proposed by W3C (http://ww.w3.org/) as a vision for the future of the Web in which information is given explicit meaning, making it easier for humans to find what they want by enabling machines to process information available on the Web. Designing and populating RDF to provide answers to commonly asked questions by users of a Web is a key step towards the establishing a Semantic Web. Recently, there have been several Web-based efforts reported We discuss our efforts towards this goal in the context of the structural data represented either as text-based or imagebased data and distributed by an AIDS structural database (http://bioinfo.nist.gov/SemanticWeb_hiv3d/chemblast.do). Organization of the information into a taxonomy tree [18] is one of the familiar concepts used to streamline the text-based information presented to a user over the Web. Here we illustrate how this technique could be extended to present images of components of chemical structures. We illustrate the limited use of Protégé for this modeling
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