A Suite of Daml+oil Ontologies to Describe Bioinformatics Web Services and Data

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 my GRID. 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.

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

“…Our choice of an RDF(S) backend has enabled development and deployment of a system with low complexity, without precluding migration to a richer semantic framework based on OWL when required. Currently, we have found that reasoning technologies are useful during construction of a domain ontology [19]. However our assessment is that there is a limited role for reasoning technologies in enabling user oriented service discovery.…”

“…The majority of the information in the data model was captured in the my Grid service ontology described previously [19]. This ontology contains substantial information describing the bioinformatics domain, which acts as an annotation vocabulary including: descriptions of the core bioinformatics data types (e.g.…”

“…This process has previously been used highly successfully in bioinformatics [2]. Due to the complexity of the domain, we choose to develop a complex property based ontology using OWL (initially DAML+OIL), which enabled us to take advantage of the reasoning at development time [19]. For use within Feta, we have reasoned over the ontology and then exported it as an RDF(S) hierarchy.…”

“…The requirement for full automation, and transparency of composition from the user perspective, has resulted in the application of extremely rich service descriptions, using description logics, or F-logic, based formalisms. In keeping with these approaches, the my Grid project has built a domain ontology for describing bioinformatics services, described services semantically using that ontology, and used description logic reasoning to support service discovery [19]. However, we found this approach bought considerable complexity to the architecture, without addressing the requirements of our target users (biologists and bioinformaticians).…”

A Taxonomy of Workflow Management Systems for Grid Computing

“…In addition, information services such as UDDI (the Universal Description, Discovery and Integration) [122] and ontology directory [134] are adopted for service discovery.…”