Collaborative development of predictive toxicology applications

Hardy, B; Douglas, N; Helma, C; Rautenberg, M; Jeliazkova, N; Jeliazkov, V; Nikolova, I; Benigni, R; Tcheremenskaia, O; Kramer, S; Girschick, T; Buchwald, F; Wicker, J; Karwath, A; Gutlein, M; Maunz, A; Sarimveis, H; Melagraki, G; Afantitis, A; Sopasakis, P; Gallagher, D; Poroikov, V; Filimonov, D; Zakharov, A; Lagunin, A; Gloriozova, T; Novikov, S; Skvortsova, N; Druzhilovsky, D; Chawla, S; Ghosh, I; Ray, S; Patel, H; Escher, S

dc.contributor.author	Hardy, B	en
dc.contributor.author	Douglas, N	en
dc.contributor.author	Helma, C	en
dc.contributor.author	Rautenberg, M	en
dc.contributor.author	Jeliazkova, N	en
dc.contributor.author	Jeliazkov, V	en
dc.contributor.author	Nikolova, I	en
dc.contributor.author	Benigni, R	en
dc.contributor.author	Tcheremenskaia, O	en
dc.contributor.author	Kramer, S	en
dc.contributor.author	Girschick, T	en
dc.contributor.author	Buchwald, F	en
dc.contributor.author	Wicker, J	en
dc.contributor.author	Karwath, A	en
dc.contributor.author	Gutlein, M	en
dc.contributor.author	Maunz, A	en
dc.contributor.author	Sarimveis, H	en
dc.contributor.author	Melagraki, G	en
dc.contributor.author	Afantitis, A	en
dc.contributor.author	Sopasakis, P	en
dc.contributor.author	Gallagher, D	en
dc.contributor.author	Poroikov, V	en
dc.contributor.author	Filimonov, D	en
dc.contributor.author	Zakharov, A	en
dc.contributor.author	Lagunin, A	en
dc.contributor.author	Gloriozova, T	en
dc.contributor.author	Novikov, S	en
dc.contributor.author	Skvortsova, N	en
dc.contributor.author	Druzhilovsky, D	en
dc.contributor.author	Chawla, S	en
dc.contributor.author	Ghosh, I	en
dc.contributor.author	Ray, S	en
dc.contributor.author	Patel, H	en
dc.contributor.author	Escher, S	en
dc.date.accessioned	2014-03-01T01:33:00Z
dc.date.available	2014-03-01T01:33:00Z
dc.date.issued	2010	en
dc.identifier.issn	1758-2946	en
dc.identifier.uri	https://dspace.lib.ntua.gr/xmlui/handle/123456789/20277
dc.subject	Application Program Interface	en
dc.subject	Chemical Structure	en
dc.subject	Communication Protocol	en
dc.subject	Controlled Vocabulary	en
dc.subject	Data Access	en
dc.subject	Data Management	en
dc.subject	Data Model	en
dc.subject	Data Representation	en
dc.subject	Experimental Data	en
dc.subject	Legislation	en
dc.subject	Open Source	en
dc.subject	Predictive Modelling	en
dc.subject	Quantitative Structure Activity Relationship	en
dc.subject	Safety Assessment	en
dc.subject	Satisfiability	en
dc.subject	Standardisation	en
dc.subject	Structure Activity Relationship	en
dc.subject	User Needs	en
dc.subject	Web Service	en
dc.title	Collaborative development of predictive toxicology applications	en
heal.type	journalArticle	en
heal.identifier.primary	10.1186/1758-2946-2-7	en
heal.identifier.secondary	http://dx.doi.org/10.1186/1758-2946-2-7	en
heal.identifier.secondary	7	en
heal.language	English	en
heal.publicationDate	2010	en
heal.abstract	OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals. The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation. Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.	en
heal.publisher	BIOMED CENTRAL LTD	en
heal.journalName	JOURNAL OF CHEMINFORMATICS	en
dc.identifier.doi	10.1186/1758-2946-2-7	en
dc.identifier.isi	ISI:000208222200006	en
dc.identifier.volume	2	en