Transparent access to multiple bioinformatics information sources

TLDR

Most bioinformatics data sources are non‑database tools with limited interfaces. The paper introduces TAMBIS, a retrieval‑based integration system that uses a domain ontology to enable biologists to access multiple bioinformatics resources. TAMBIS employs a description‑logic ontology managed by a terminology server to drive a visual query interface and to rewrite declarative queries into source‑specific requests executed by middleware. The ontology centralizes interoperation among tools, and a Java applet pilot integrating five protein sources is in field trials, demonstrating the system’s ability to answer real biological questions.

Abstract

This paper describes the Transparent Access to Multiple Bioinformatics Information Sources project, known as TAMBIS, in which a domain ontology for molecular biology and bioinformatics is used in a retrieval-based information integration system for biologists. The ontology, represented using a description logic and managed by a terminology server, is used both to drive a visual query interface and as a global schema against which complex intersource queries are expressed. These source-independent declarative queries are then rewritten into collections of ordered source-dependent queries for execution by a middleware layer. In bioinformatics, the majority of data sources are not databases but tools with limited accessible interfaces. The ontology helps manage the interoperation between these resources. The paper emphasizes the central role that is played by the ontology in the system. The project distinguishes itself from others in the following ways: the ontology, developed by a biologist, is substantial; the retrieval interface is sophisticated; the description logic is managed by a sophisticated terminology server. A full pilot application is available as a Java™ applet integrating five sources concerned with proteins. This pilot is currently undergoing field trials with working biologists and is being used to answer real questions in biology, one of which is used as a case study throughout the paper.