Computational toxicology using the OpenTox application programming interface and Bioclipse

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Willighagen, Egon L ^a,b   Jeliazkova, Nina ^c   Hardy, Barry ^d   Grafström, Roland C ^b,e   Spjuth, Ola ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c IDEACONSULT LTD   (Bulgaria)

^d Douglas Connect ^*  (Switzerland)

^e VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80755142997     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-487     Document Type: Article

References (36)

1. Diderichs R, Tools for Category Formation and Read-Across: Overview of the OECD (Q)SAR Application Toolbox The Royal Society of Chemistry 2010 385 407 chap 16
2. QSAR ToolBox. http://www.qsartoolbox.org/
3. An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B, SAR and QSAR in environmental research 2008 19 5-6 495 524 10.1080/10629360802083871 18853299
4. ToxTree. http://toxtree.sourceforge.net/
5. Bioclipse: An open source workbench for chemo- and bioinformatics. Spjuth O, Helmus T, Willighagen E, Kuhn S, Eklund M, Wagener J, Rust PM, Steinbeck C, Wikberg J, BMC Bioinformatics 2007 8
6. Bioclipse 2: A scriptable integration platform for the life sciences. Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen E, Steinbeck C, Wikberg J, BMC Bioinformatics 2009 10 397 10.1186/1471-2105-10-397 19958528
7. Integrated Decision Support for Assessing Chemical Liabilities. Spjuth O, Eklund M, Ahlberg Helgee E, Boyer S, Carlsson L, Journal of Chemical Information and Modeling 2011 51 8 1840 1847 10.1021/ci200242c 21774475
8. 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 Ta, Novikov S, Skvortsova N, Druzhilovsky D, Chawla S, Ghosh I, Ray S, Patel H, Escher S, Journal of Cheminformatics 2010 2 7 10.1186/1758-2946-2-7 20807436
9. Activity profiles of 309 ToxCast chemicals evaluated across 292 biochemical targets. Knudsen TB, Houck KA, Sipes NS, Singh AV, Judson RS, Martin MT, Weissman A, Kleinstreuer NC, Mortensen HM, Reif DM, Rabinowitz JR, Setzer RW, Richard AM, Dix DJ, Kavlock RJ, Toxicology 2011 282 1-2 1 15 10.1016/j.tox.2010.12.010 21251949
10. SuperToxic: a comprehensive database of toxic compounds. Schmidt U, Struck S, Gruening B, Hossbach J, Jaeger IS, Parol R, Lindequist U, Teuscher E, Preissner R, Nucleic Acids Research 2009 37 suppl 1 295 D299 19004875
11. A side effect resource to capture phenotypic effects of drugs. Kuhn M, Campillos M, Letunic I, Jensen LJJ, Bork P, Molecular systems biology 2010 6 343
12. DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages. Williams-DeVane CR, Wolf MA, Richard AM, Bioinformatics 2009 25 5 692 694 10.1093/bioinformatics/btp042 19158160
13. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Huang DW, Sherman BT, Lempicki RA, Nature protocols 2009 4 44 57 19131956
14. KEGG: Kyoto Encyclopedia of Genes and Genomes. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M, Nucleic acids research 1999 27 29 34 10.1093/nar/27.1.29 9847135 (Pubitemid 29209394)
15. Mining Biological Pathways Using WikiPathways Web Services. Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR, PLoS ONE 2009 4 7 6447+ 19649250
16. The SMARTCyp cytochrome P450 metabolism prediction server. Rydberg P, Gloriam DE, Olsen L, Bioinformatics 2010 26 23 2988 2989 10.1093/bioinformatics/ btq584 20947523
17. Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, amending Directive 1999/45/EC and repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC. European Parliament C, Tech rep 2006 http://eur-lex.europa.eu/ LexUriServ/LexUriServ.do?uri=CELEX:32006R1907:en:NOT
18. AMBIT RESTful web services: an implementation of the OpenTox application programming interface. Jeliazkova N, Jeliazkov V, Journal of Cheminformatics 2011 3 18 10.1186/1758-2946-3-18 21575202
19. Resource Description Framework (RDF): Concepts and Abstract Syntax. Carroll JJ, Klyne G, 2004 http://www.w3.org/TR/2004/REC-rdf-concepts-20040210/
20. SPARQL Query Language for RDF. Prud'hommeaux E, Seaborne A, Tech rep, World-Wide-Web Consortium 2008 http://www.w3.org/TR/rdf-sparql-query/
21. Linking the Resource Description Framework to cheminformatics and proteochemometrics. Willighagen E, Alvarsson J, Andersson A, Eklund M, Lampa S, Lapins M, Spjuth O, Wikberg J, Journal of Biomedical Semantics 2011 2 Suppl 1 6 10.1186/2041-1480-2-S1-S6 21624161
22. Towards interoperable and reproducible QSAR analyses: Exchange of datasets. Spjuth O, Willighagen E, Guha R, Eklund M, Wikberg J, Journal of Cheminformatics 2010 2 5 10.1186/1758-2946-2-5 20591161
23. BioCatalogue: a universal catalogue of web services for the life sciences. Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA, Nucleic Acids Research 2010 38 suppl 2 689 W694 http://dx.doi.org/10.1093/nar/gkq394 20484378
24. OWL 2 Web Ontology Language Document Overview. W3C OWL Working Group, Tech rep, W3C 2009 Http://www.w3.org/TR/2009/REC-owl2-overview-20091027/
25. Recent developments of the chemistry development kit (CDK)-an open-source java library for chemo- and bioinformatics. Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL, Current pharmaceutical design 2006 12 17 2111 2120 10.2174/138161206777585274 16796559 (Pubitemid 43891407)
26. CC0 1.0 Universal Public Domain Dedication. http://creativecommons.org/ publicdomain/zero/1.0/
27. ODC Public Domain Dedication and Licence 1.0. http://www.opendatacommons. org/licenses/pddl/1-0/
28. Open Database License 1.0. http://opendatacommons.org/licenses/odbl/1.0/
29. Open Data Commons Attribution License 1.0. http://opendatacommons.org/ licenses/by/1.0/
30. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D, Nucleic Acids Res 2010 38 Suppl 677 82 20501605
31. ToxPredict. Ideaconsult Ltd, http://toxpredict.org/
32. Taverna: a tool for the composition and enactment of bioinformatics workflows. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P, Bioinformatics 2004 20 17 3045 3054 10.1093/bioinformatics/bth361 15201187 (Pubitemid 39619196)
33. Advancing translational research with the Semantic Web. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong G, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH, BMC Bioinformatics 2007 8 Suppl 3 2 10.1186/1471-2105-8-S3-S2 18269696 (Pubitemid 351833772)
34. Biomedical semantics in the Semantic Web. Splendiani A, Burger A, Paschke A, Romano P, Marshall M, Journal of Biomedical Semantics 2011 2 Suppl 1 1 10.1186/2041-1480-2-S1-S1 21995847
35. Resource description framework technologies in chemistry. Willighagen EL, Brändle MP, Journal of Cheminformatics 2011 3 15 10.1186/1758-2946-3-15 21569523
36. Semantic Web integration of cheminformatics resources with the SADI framework. Chepelev L, Dumontier M, Journal of Cheminformatics 2011 3 16 10.1186/1758-2946-3-16 21575200