Computational toxicology using the OpenTox application programming interface and Bioclipse

BackgroundToxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications.FindingsThis article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources.ConclusionsA novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.

[1]  Ola Spjuth,et al.  Integrated Decision Support for Assessing Chemical Liabilities , 2011, J. Chem. Inf. Model..

[2]  Egon L. Willighagen,et al.  Bioclipse 2: A scriptable integration platform for the life sciences , 2009, BMC Bioinformatics.

[3]  C. Steinbeck,et al.  Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. , 2006, Current pharmaceutical design.

[4]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[5]  Ulrike Schmidt,et al.  SuperToxic: a comprehensive database of toxic compounds , 2008, Nucleic Acids Res..

[6]  Michel Dumontier,et al.  Semantic Web integration of Cheminformatics resources with the SADI framework , 2011, J. Cheminformatics.

[7]  P. Bork,et al.  A side effect resource to capture phenotypic effects of drugs , 2010, Molecular systems biology.

[8]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[9]  Jeremy J. Carroll,et al.  Resource description framework (rdf) concepts and abstract syntax , 2003 .

[10]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[11]  Alexander R. Pico,et al.  Mining Biological Pathways Using WikiPathways Web Services , 2009, PloS one.

[12]  Egon L. Willighagen,et al.  Linking the Resource Description Framework to cheminformatics and proteochemometrics , 2011, J. Biomed. Semant..

[13]  Egon L. Willighagen,et al.  Bioclipse: an open source workbench for chemo- and bioinformatics , 2007, BMC Bioinformatics.

[14]  Egon L. Willighagen,et al.  Resource description framework technologies in chemistry , 2011, J. Cheminformatics.

[15]  G. Patlewicz,et al.  An evaluation of the implementation of the Cramer classification scheme in the Toxtree software , 2008, SAR and QSAR in environmental research.

[16]  Pantelis Sopasakis,et al.  Collaborative development of predictive toxicology applications , 2010, J. Cheminformatics.

[17]  Carole A. Goble,et al.  myExperiment: a repository and social network for the sharing of bioinformatics workflows , 2010, Nucleic Acids Res..

[18]  Kei-Hoi Cheung,et al.  Advancing translational research with the Semantic Web , 2007, BMC Bioinformatics.

[19]  Carole A. Goble,et al.  BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..

[20]  Nina Jeliazkova,et al.  AMBIT RESTful web services: an implementation of the OpenTox application programming interface , 2011, J. Cheminformatics.

[21]  In-Seok Gang,et al.  VTT-Technical Research Center of Finland , 2002 .

[22]  E. Prud hommeaux,et al.  SPARQL query language for RDF , 2011 .

[23]  David E. Gloriam,et al.  The SMARTCyp cytochrome P450 metabolism prediction server , 2010, Bioinform..

[24]  David M. Reif,et al.  Activity profiles of 309 ToxCast™ chemicals evaluated across 292 biochemical targets. , 2011, Toxicology.

[25]  Ann M. Richard,et al.  DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages , 2009, Bioinform..

[26]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[27]  Egon L. Willighagen,et al.  Towards interoperable and reproducible QSAR analyses: Exchange of datasets , 2010, J. Cheminformatics.

[28]  R. Diderichs.  Chapter 16:Tools for Category Formation and Read-Across: Overview of the OECD (Q)SAR Application Toolbox , 2010 .

[29]  Andrea Splendiani,et al.  Biomedical semantics in the Semantic Web , 2011, J. Biomed. Semant..