A SUITE OF DAML+OIL ONTOLOGIES TO DESCRIBE BIOINFORMATICS WEB SERVICES AND DATA

TLDR

The expanding volume and distribution of bioinformatics resources requires expert knowledge to locate and integrate them into workflows, and different activities demand distinct knowledge representations, with service discovery best supported by classification and configuration best achieved through formal descriptions, yet these interdependent representations are difficult to maintain manually. The study aims to formally capture bioinformatics knowledge in a virtual workbench and middleware framework, reporting a description‑logic approach with DAML‑OIL property‑based service descriptions, and detailing extensions to DAML‑S for bioinformatics service description, dynamic classification, and a DAML‑OIL ontology service that supports partial user‑driven matching and composition. The ontology, built on DAML‑S, uses property‑based service descriptions to dynamically create classifications that enable semantic service matching and discovery within a large grid‑based middleware project. These classifications.

Abstract

The growing quantity and distribution of bioinformatics resources means that finding and utilizing them requires a great deal of expert knowledge, especially as many resources need to be tied together into a workflow to accomplish a useful goal. We want to formally capture at least some of this knowledge within a virtual workbench and middleware framework to assist a wider range of biologists in utilizing these resources. Different activities require different representations of knowledge. Finding or substituting a service within a workflow is often best supported by a classification. Marshalling and configuring services is best accomplished using a formal description. Both representations are highly interdependent and maintaining consistency between the two by hand is difficult. We report on a description logic approach using the web ontology language DAML+OIL that uses property based service descriptions. The ontology is founded on DAML-S to dynamically create service classifications. These classifications are then used to support semantic service matching and discovery in a large grid based middleware project [Formula: see text]. We describe the extensions necessary to DAML-S in order to support bioinformatics service description; the utility of DAML+OIL in creating dynamic classifications based on formal descriptions; and the implementation of a DAML+OIL ontology service to support partial user-driven service matching and composition.