AMBIT RESTful web services: An implementation of the OpenTox application programming interface

Journal of Cheminformatics

Volumn 3, Issue 1, 2011, Pages

  Jeliazkova, Nina ^a   Jeliazkov, Vedrin ^a  

^a IDEACONSULT LTD   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959719819     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-3-18     Document Type: Article

References (65)

1. Collaborative Development of Predictive Toxicology Applications. B Hardy N Douglas C Helma M Rautenberg N Jeliazkova V Jeliazkov I Nikolova R Benigni O Tcheremenskaia S Kramer T Girschick F Buchwald J Wicker A Karwath M Gütlein A Maunz H Sarimveis G Melagraki A Afantitis P Sopasakis D Gallagher V Poroikov D Filimonov A Zakharov A Lagunin T Gloriozova S Novikov N Skvortsova D Druzhilovsky S Chawla I Ghosh S Ray H Patel S Escher, J Cheminform 2010 2 7 10.1186/1758-2946-2-7 20807436
2. Resource Description Framework. http://www.w3.org/RDF/
3. R. Fielding, Representational State Transfer (REST). http://www.ics.uci. edu/∼fielding/pubs/dissertation/rest-arch-style.htm
4. RESTful Web Services. L Richardson S Ruby, Sebastopol, CA, USA: O'Reilly Media, Inc 2007
5. OASIS Standards. http://www.oasis-open.org/specs/
6. RFC 2616 Hypertext Transfer Protocol - HTTP/1.1. http://tools.ietf.org/ html/rfc2616
7. RFC 5023 The Atom Publishing Protocol. http://tools.ietf.org/html/rfc5023
8. OpenTox ontology. http://opentox.org/api/1.1/opentox.owl
9. RDF/XML Syntax Specification. http://www.w3.org/TR/REC-rdf-syntax/
10. Notation 3 (N3) A Readable RDF Syntax. http://www.w3.org/DesignIssues/ Notation3
11. Turtle - Terse RDF Triple Language. http://www.w3.org/TeamSubmission/ turtle/
12. OWL Web Ontology Language Guide. http://www.w3.org/TR/owl-guide/
13. Microformats. http://microformats.org/
14. AMBIT project. http://ambit.sourceforge.net/
15. Chapter 17. Open Source Tools for Read-Across and Category Formation. N Jeliazkova J Jaworska A Worth, In Silico Toxicology : Principles and Applications Madden J.: Cambridge: RSC Publishing, Cronin M, 2010 408 445
16. MySQL. http://www.mysql.com/
17. CEFIC Long Range research initiative. http://www.cefic-lri.org/
18. Apache Tomcat. http://tomcat.apache.org/
19. Java Servlet Technology. http://www.oracle.com/technetwork/java/index- jsp-135475.html
20. Toxtree. http://toxtree.sourceforge.net/
21. An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. G Patlewicz N Jeliazkova RJ Safford AP Worth B Aleksiev, SAR QSAR Environ Res 2008 19 5-6 495 524 18853299
22. Implementation of simple OpenTox Ontology service. https://ambit.svn. sourceforge.net/svnroot/ambit/branches/opentox/ontology-service
23. The Chemistry Development Kit. http://cdk.sourceforge.net/
24. The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. C Steinbeck Y Han S Kuhn O Horlacher E Luttmann EL Willighagen, J Chem Inf Comput Sci 43 2 493 500
25. Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo-and Bioinformatics. C Steinbeck C Hoppe S Kuhn M Floris R Guha EL Willighagen, Curr Pharm 2006 12 17 2111 2120 10.2174/138161206777585274 (Pubitemid 43891407)
26. Restlet, REST framework for Java. http://www.restlet.org/
27. Jena - A Semantic Web Framework for Java. http://jena.sourceforge.net/
28. Apache Maven. http://maven.apache.org/
29. AMBIT source code. https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ ambit2-all
30. Toxtree - Toxic Hazard Estimation by decision tree approach, source code. https://toxtree.svn.sourceforge.net/svnroot/toxtree/trunk/toxtree
31. OpenTox API wiki site. http://opentox.org/dev/apis/
32. Chemical MIME. http://chemical-mime.sourceforge.net/
33. cURL tool. http://curl.haxx.se/
34. ToxCast - Predicting Hazard, Characterizing Toxicity Pathways, and Prioritizing the Toxicity Testing of Environmental Chemicals. http://www.epa.gov/ncct/toxcast/
35. TDB - A SPARQL Database for Jena. http://openjena.org/TDB/
36. Restlet documentation on ServerResource class. http://www.restlet.org/ documentation/2.0/jee/api/org/restlet/resource/ServerResource.html
37. The Streaming API for XML. http://stax.codehaus.org/
38. JDK Documentation. http://download.oracle.com/javase/6/docs/api/java/ util/concurrent/Callable.html
39. JSON (JavaScript Object Notation). http://www.json.org/
40. CPDBAS: Carcinogenic Potency Database Summary Tables. http://www.epa.gov/ncct/dsstox/sdf-cpdbas.html
41. ISSCAN: Chemical Carcinogens Database. http://www.iss.it/ampp/dati/cont. php?id=233&lang=1&tipo=7
42. ToxML. http://www.leadscope.com/toxml.php
43. ToxML project. https://www.lhasalimited.org/research/toxml
44. The Open Biological and Biomedical Ontologies. http://www.obofoundry.org/
45. MIBBI: Minimum Information for Biological and Biomedical Investigations. http://www.mibbi.org/
46. Guidance on information requirements and chemical safety assessment Chapter R.6: QSARs and grouping of chemicals. http://guidance.echa.europa.eu/ docs/guidance-document/information-requirements-r6-en.pdf?vers=20-08-08
47. GO Ontology. http://www.geneontology.org/
48. J Day, Patterns in Network Architecture: A Return to Fundamentals Upper Saddle River, New Jersey, USA: Prentice Hall 2007
49. An evaluation of approaches to federated query processing over linked data. P Haase T Mathä M Ziller, I-SEMANTICS '10 Proceedings of the 6th International Conference on Semantic Systems ACM New York, NY, USA 2010 21574749
50. Active Knowledge: Dynamically Enriching RDF Knowledge Bases by Web Services, Proceeding. N Preda G Kasneci FM Suchanek T Neumann W Yuan G Weikum, SIGMOD '10 Proceedings of the 2010 international conference on Management of data ACM New York, NY, USA 2010
51. WEKA - Machine learning in Java. http://www.cs.waikato.ac.nz/ml/weka/
52. SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism. P Rydberg DE Gloriam J Zaretzki C Breneman L Olsen, ACS Med Chem Lett., 2010 1 3 96 100 10.1021/ml100016x
53. pKa Prediction of Monoprotic Small Molecules the SMARTS Way. AC Lee JY Yu GM Crippen, J Chem Inf Model., 2008 48 10 2042 2053 10.1021/ci8001815
54. How can structural similarity analysis help in category formation. J Jaworska N Nikolova-Jeliazkova, SAR and QSAR in Environmental Research 2007 18 3-4 195 207 17514565 (Pubitemid 46789491)
55. QSAR Applicability Domain Estimation by Projection of the Training Set in Descriptor Space: A Review. J Jaworska N Nikolova-Jeliazkova T Aldenberg, Altern Lab Anim 2005 33 445 459 16268757 (Pubitemid 41613738)
56. Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52. TI Netzeva A Worth T Aldenberg R Benigni MT Cronin P Gramatica JS Jaworska S Kahn G Klopman CA Marchant G Myatt N Nikolova-Jeliazkova GY Patlewicz R Perkins D Roberts T Schultz DW Stanton JJ van de Sandt W Tong G Veith C Yang, Altern Lab Anim 2005 33 155 173 16180989 (Pubitemid 40686385)
57. Site of metabolism prediction for six biotransformations mediated by cytochromes P450. M Zheng X Luo Q Shen Y Wang Y Du W Zhu H Jiang, Bioinformatics 2009 25 10 1251 1258 10.1093/bioinformatics/btp140 19286831
58. SADI framework. http://sadiframework.org/
59. SADI, SHARE, and the in silico scientific method. MD Wilkinson L McCarthy B Vandervalk D Withers E Kawas S Samadian, 11th Annual Bioinformatics Open Source Conference (BOSC) 2010, Boston, MA, USA 2010 http://www.biomedcentral. com/content/pdf/1471-2105-11-s12-s7.pdf
60. SHARE: A Semantic Web Query Engine for Bioinformatics. B Vandervalk L McCarthy MD Wilkinson, The Semantic Web, Lecture Notes in Computer Science proceedings of the ASWC 2009 5926 367 369 10.1007/978-3-642-10871-6-27
61. ToxPredict demo application. http://toxpredict.org/
62. OpenTox Authentication and Authorisation API. http://opentox.org/dev/ apis/api-1.2/AA
63. OpenAM. http://www.forgerock.com/openam.html
64. Wikipedia entry for Linked Data. http://en.wikipedia.org/wiki/Linked-Data
65. Possible Ontologies: How Reality Constrains the Development of Relevant Ontologies. M Hepp, IEEE Internet Computing 2007 11 1 90 96 (Pubitemid 46332150)