title: A toxicology ontology roadmap.
abstract: Foreign substances can have a dramatic and unpredictable adverse effect on human health. In the development of new therapeutic agents, it is essential that the potential adverse effects of all candidates be identified as early as possible. The field of predictive toxicology strives to profile the potential for adverse effects of novel chemical substances before they occur, both with traditional in vivo experimental approaches and increasingly through the development of in vitro and computational methods which can supplement and reduce the need for animal testing. To be maximally effective, the field needs access to the largest possible knowledge base of previous toxicology findings, and such results need to be made available in such a fashion so as to be interoperable, comparable, and compatible with standard toolkits. This necessitates the development of open, public, computable, and standardized toxicology vocabularies and ontologies so as to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. Such ontology development will support data management, model building, integrated analysis, validation and reporting, including regulatory reporting and alternative testing submission requirements as required by guidelines such as the REACH legislation, leading to new scientific advances in a mechanistically-based predictive toxicology.  Numerous existing ontology and standards initiatives can contribute to the creation of a toxicology ontology supporting the needs of predictive toxicology and risk assessment. Additionally, new ontologies are needed to satisfy practical use cases and scenarios where gaps currently exist. Developing and integrating these resources will require a well-coordinated and sustained effort across numerous stakeholders engaged in a public-private partnership. In this communication, we set out a roadmap for the development of an integrated toxicology ontology, harnessing existing resources where applicable. We describe the stakeholders' requirements analysis from the academic and industry perspectives, timelines, and expected benefits of this initiative, with a view to engagement with the wider community.
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: D000826:Animal Testing Alternatives; D000818:Animals; D019295:Computational Biology; D016208:Databases, Factual; D006801:Humans; D012106:Research; D018570:Risk Assessment; D014116:Toxicology / Q000191:economics / Q000331:legislation & jurisprudence / Q000379:methods*; D018875:Vocabulary, Controlled