title: Toxicology ontology perspectives.
abstract: The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. In this article we review ontology developments based on a set of perspectives showing how ontologies are being used in predictive toxicology initiatives and applications. Perspectives on resources and initiatives reviewed include OpenTox, eTOX, Pistoia Alliance, ToxWiz, Virtual Liver, EU-ADR, BEL, ToxML, and Bioclipse. We also review existing ontology developments in neighboring fields that can contribute to establishing an ontological framework for predictive toxicology. A significant set of resources is already available to provide a foundation for an ontological framework for 21st century mechanistic-based toxicology research. Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated in an extended future framework. OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources. Bioclipse developers have shown the benefit of interoperability obtained through ontology by being able to link their workbench application with remote OpenTox web services. Although these developments are promising, an increased international coordination of efforts is greatly needed to develop a more unified, standardized, and open toxicology ontology framework.
authors.affiliation: Douglas Connect and OpenTox, Zeiningen, Switzerland. Barry.Hardy@douglasconnect.com
authors.forename: Barry
authors.initials: B
authors.lastname: Hardy
authors.forename: Gordana
authors.initials: G
authors.lastname: Apic
authors.forename: Philip
authors.initials: P
authors.lastname: Carthew
authors.forename: Dominic
authors.initials: D
authors.lastname: Clark
authors.forename: David
authors.initials: D
authors.lastname: Cook
authors.forename: Ian
authors.initials: I
authors.lastname: Dix
authors.forename: Sylvia
authors.initials: S
authors.lastname: Escher
authors.forename: Janna
authors.initials: J
authors.lastname: Hastings
authors.forename: David J
authors.initials: DJ
authors.lastname: Heard
authors.forename: Nina
authors.initials: N
authors.lastname: Jeliazkova
authors.forename: Philip
authors.initials: P
authors.lastname: Judson
authors.forename: Sherri
authors.initials: S
authors.lastname: Matis-Mitchell
authors.forename: Dragana
authors.initials: D
authors.lastname: Mitic
authors.forename: Glenn
authors.initials: G
authors.lastname: Myatt
authors.forename: Imran
authors.initials: I
authors.lastname: Shah
authors.forename: Ola
authors.initials: O
authors.lastname: Spjuth
authors.forename: Olga
authors.initials: O
authors.lastname: Tcheremenskaia
authors.forename: Luca
authors.initials: L
authors.lastname: Toldo
authors.forename: David
authors.initials: D
authors.lastname: Watson
authors.forename: Andrew
authors.initials: A
authors.lastname: White
authors.forename: Chihae
authors.initials: C
authors.lastname: Yang
mesh_terms: D000818:Animals; D016208:Databases, Factual; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D014116:Toxicology / Q000379:methods*; D018875:Vocabulary, Controlled