A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using Daml+oil

Abstract

The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal expressiveness and the reasoning capabilities of the underlying description logic. Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology. The paper introduces DAML+OIL and demonstrates the activity within each stage of the methodology and the functionality gained.

The OWL Instance Store: System Description

“…Extensions in the structure of the ontology (as envisaged in GONG [17]) would allow more complex assertions to be made and more complex queries to be asked .…”

A Method for Converting Thesauri to RDF/OWL

“…The properties are hierarchically organized using rdfs:subPropertyOf according to the qualifier hierarchy. Wroe et al [16] describe a methodology to migrate the Gene Ontology (GO) from XML to DAML+OIL. Their goal is to "support validation, extension and multiple classification" of the GO.…”

“…Additionally, work is in progress to produce a guideline document on converting multilingual thesauri. 16 The development of a standard schema influences our standardization step, and guidelines on converting multilingual thesauri may be incorporated to broaden the scope of our method.…”

Modularisation of domain ontologies implemented in description logics and related formalisms including OWL

“…OpenGALEN 3 [9], SNOMED-RT/CT 4 [16], and in recent work in bioinformatics e.g. [21] and in many other fields. While much other work on ontologies concentrates on general issues of development, e.g.…”