A semantic web ontology for small molecules and their biological targets

Journal of Chemical Information and Modeling

Volumn 50, Issue 5, 2010, Pages 732-741

  Choi, Jooyoung ^a   Davis, Melissa J ^a   Newman, Andrew F ^a   Ragan, Mark A ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; GENES; MOLECULAR BIOLOGY; MOLECULES; ONTOLOGY;

BIOLOGICAL PROPERTIES; BIOMEDICAL RESEARCH; PHARMACOLOGICAL RESEARCH; PUBLIC DATA SOURCE; RESOURCE DESCRIPTION FRAMEWORK; SEMANTIC WEB ONTOLOGIES; SEMANTIC WEB TECHNOLOGY; WEB ONTOLOGY LANGUAGE;

SEMANTIC WEB;

ARTICLE; BIOLOGY; DATA BASE; DRUG DEVELOPMENT; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; NATURAL LANGUAGE PROCESSING; SEMANTICS;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DRUG DISCOVERY; INFORMATION STORAGE AND RETRIEVAL; INTERNET; NATURAL LANGUAGE PROCESSING; SEMANTICS;

EID: 77952767685     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900461j     Document Type: Article

References (47)

1. Baker, C. J. O.; Cheung, K.-H. Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, 1st ed.; Springer: New York, NY, 2007.
2. Manola, F.; Miller, E. RDF Primer; World Wide Web Consortium: Cambridge, MA; Sophia-Antipolis, France; and Tokyo, Japan; http://www.w3.org/TR/2004/REC- rdf-primer-20040210/. Accessed February 28, 2010.
3. McGuinness, D. L.; Harmelen, F. V. OWL Web Ontology Language Overview; World Wide Web Consortium: Cambridge, MA; Sophia-Antipolis, France; and Tokyo, Japan; http://www.w3.org/TR/2004/REC-owl-features-20040210/. Accessed February 28, 2010.
4. Smith, M. K.; Welty, C.; McGuinness, D. L. OWL Web Ontology Language Guide; World Wide Web Consortium: Cambridge, MA; Sophia-Antipolis, France; and Tokyo, Japan; http://www.w3.org/TR/2004/REC-owl-guide-20040210/. Accessed February 28, 2010.
5. Dumontier, M.; Villanueva-Rosales, N. Towards pharmacogenomics knowledge discovery with the semantic web Briefings Bioinf. 2009, 10 (2) 153-63
6. Chen, H.; Ding, L.; Wu, Z.; Yu, T.; Dhanapalan, L.; Chen, J. Y. Semantic web for integrated network analysis in biomedicine Briefings Bioinf. 2009, 10 (2) 177-92
7. Ruttenberg, A.; Rees, J. A.; Samwald, M.; Marshall, M. S. Life sciences on the Semantic Web: the Neurocommons and beyond Briefings Bioinf. 2009, 10 (2) 193-204
8. Das, S.; Girard, L.; Green, T.; Weitzman, L.; Lewis-Bowen, A.; Clark, T. Building biomedical web communities using a semantically aware content management system Briefings Bioinf. 2009, 10 (2) 129-38
9. Belleau, F.; Nolin, M. A.; Tourigny, N.; Rigault, P.; Morissette, J. Bio2RDF: towards a mashup to build bioinformatics knowledge systems J. Biomed. Inf. 2008, 41 (5) 706-16
10. Butcher, E. C.; Berg, E. L.; Kunkel, E. J. Systems biology in drug discovery Nat. Biotechnol. 2004, 22 (10) 1253-9
11. Fullbeck, M.; Michalsky, E.; Dunkel, M.; Preissner, R. Natural products: sources and databases Nat. Prod. Rep. 2006, 23 (3) 347-56
12. Degtyarenko, K.; de Matos, P.; Ennis, M.; Hastings, J.; Zbinden, M.; McNaught, A.; Alcantara, R.; Darsow, M.; Guedj, M.; Ashburner, M. ChEBI: a database and ontology for chemical entities of biological interest Nucleic Acids Res. 2008, 36 (Database issue) D344-50
13. Seiler, K. P.; George, G. A.; Happ, M. P.; Bodycombe, N. E.; Carrinski, H. A.; Norton, S.; Brudz, S.; Sullivan, J. P.; Muhlich, J.; Serrano, M.; Ferraiolo, P.; Tolliday, N. J.; Schreiber, S. L.; Clemons, P. A. ChemBank: a small-molecule screening and cheminformatics resource database Nucleic Acids Res. 2008, 36 (Database issue) D351-9
14. Murray-Rust, P.; Mitchell, J. B.; Rzepa, H. S. Chemistry in bioinformatics BMC Bioinformatics 2005, 6, 141
15. Feldman, H. J.; Dumontier, M.; Ling, S.; Haider, N.; Hogue, C. W. CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules FEBS Lett. 2005, 579 (21) 4685-91
16. Degtyarenko, K.; Hastings, J.; de Matos, P.; Ennis, M. ChEBI: an open bioinformatics and cheminformatics resource Curr. Protoc. Bioinformatics 2009, 14.9.1-14.9.20 Chapter 14
17. Varadwaj, P. K.; Lahiri, T. FGO: A novel ontology for identification of ligand functional group Bioinformation 2007, 2 (3) 113-8
18. Frey, J.; Roure, D. D.; Taylor, K.; Essex, J.; Mills, H.; Zaluska, E. CombeChem: A Case Strudy in Provenance and Annotation Using the Semantic Web; Springer Berlin: Heidelberg, Germany, 2006; Vol. 4145/2006, p 270 - 277.
19. Taylor, K.; Gledhill, R.; Essex, J.; Frey, J. Bringing Chemical Data onto the Semantic Web J. Chem. Inf. Model. 2006, 46, 939-952
20. Bechhofer, S.; van Harmelen, F.; Hendler, J.; Horrocks, I.; McGuinness, D. L.; Petel-Schneider, P. F.; Stein, L. A. OWL Web Ontology Language Reference; World Wide Web Consortium: Cambridge, MA; Sophia-Antipolis, France; and Tokyo, Japan; http://www.w3.org/TR/2004/REC-owl-ref-20040210/. Accessed February 28, 2010.
21. Horrocks, I.; Patel-Schneider, P. F.; Harmelen, F. From SHIQ and RDF to OWL: the making of a Web Ontology Language J. Web Semant. 2003, 1, 7-26
22. Prud'hommeaux, E.; Seaborne, A.. SPARQL Query Language for RDF; World Wide Web Consortium: Cambridge, MA; Sophia-Antipolis, France; and Tokyo, Japan, 2006.
23. Gruninger, M.; Fox, M. S. In Methodology for the design of ontologies and evaluation of ontologies, Workshop on Basic Ontological Issues in Knowledge Sharing, IJCAI-95 Montreal, 1995; Montreal, 1995.
24. Fernandez, M.; Gomez-Perez, A.; Juristo, N. In METHONTOLOGY: From ontological art towards ontological engineering, AAAI97Spring Symposium Series, Standford, USA, 1997; Stanford, USA, 1997; pp 33 - 40.
25. Uschold, M.; Gruninger, M. Ontologies: Principles, methods and applications Knowl. Eng. Rev. 1996, 11, 93-136
26. Uschold, M.; King, M. In Towards a methodology for building ontologies, International Joint Conference on Artificial Intelligence, 1995.
27. Yu, A. C. Methods in biomedical ontology J. Biomed. Inform. 2006, 39 (3) 252-66
28. Noy, N. F.; McGuinness, D. L. Ontology Development 101: A Guide to Creating Your First Ontology; Stanford Knowledge Systems Laboratory Technical Report KSL-01-05; Stanford University: Palo Alto, CA, 2001, 2001; pp 1 - 25.
29. Gomez-Perez, A.; Fernandez-Lopez, M.; Corcho, O. Ontological Engineering with examples from the areas of Knowledge Management, e-Commerce and the Semantic Web, 2nd ed.; Springer: London, 2004.
30. Corcho, O.; Fernandez-Lopez, M.; Gomez-Perez, A. Methodologies, tools and languages for building ontologies. Where is their meeting point Data Knowl. Eng. 2003, 46, 41-64
31. Jones, D. M.; Bench-Capon, T. J. M.; Visser, P. R. S. In Methodologies for ontology development; Proceedings ITi and KNOWS Conference, 15th IFIP World Computer Congress, 1998; Chapman and Hall: London, England, 1998; pp 62 - 75.
32. Pinto, H.; Martins, J. In Reusing ontologies; AAAI Press: Menlo Park, CA, 2000; pp 77 - 84.
33. Pinto, H.; Martins, J. In A methodology for ontology integration, International Conference on Knowledge Capture (K-CAP2001), New York, New York, 2001; ACM Press: New York, 2001; pp 131 - 138.
34. Rubin, D. L.; Noy, N. F.; Musen, M. A. Protege: a tool for managing and using terminology in radiology applications J. Digit. Imaging 2007, 20 (Suppl 1) 34-46
35. Davis, M. J.; Newman, A.; Khan, I.; Hunter, J.; Ragan, M. A. In Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions, Asia-Pacific Bioinformatics Conference, Kyoto, Japan, 2008 Brazma, A.; Miyano, S.; Akutsu, T., Eds.; World Scientific Publishing Company: Kyoto, Japan, 2008; pp 145 - 154.
36. Wishart, D. S. DrugBank: a comprehensive resource for in silico drug discovery and exploration Nucleic Acids Res. 2006, 34 (Database Issue) 668-672
37. Wishart, D. S.; Knox, C.; Guo, A. C.; Cheong, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. DrugBank: a knowledgebase for drugs, drug actions and drug targets Nucleic Acids Res. 2007, 36 (Database issue) D901-D906
38. Gomez-Perez, F. Evaluation of Ontologies Int. J. Intell. Syst. 2001, 16, 391-409
39. Sirin, E.; Parsia, B.; Grau, B. C.; Kalyanpur, A.; Karz, Y. Pellet: A practical OWL-DL reasoner J. Web Semant. 2007, 5, 51-53
40. Splendiani, A. RDFScape: Semantic Web meets systems biology BMC Bioinformatics 2008, 9, S6
41. Ciccarese, P.; Wu, E.; Wong, G.; Ocana, M.; Kinoshita, J.; Ruttenberg, A.; Clark, T. The SWAN biomedical discourse ontology J. Biomed. Inform. 2008, 41 (5) 739-51
42. Pasquier, C. Biological data integration using Semantic Web technologies Biochimie 2008, 90 (4) 584-94
43. Schulze-Kremer, S. Ontologies for molecular biology and bioinformatics In Silico Biol. 2002, 2 (3) 179-93
44. Villanueva-Rosales, N.; Dumontier, M. Towards pharmacogenomics knowledge discovery with the semantic web Briefings Bioinf. 2008, 10, 153-163
45. Horrocks, I.; Petel-Schneider, P. F.; Boley, H.; Tabet, S.; Grosof, B.; Dean, M. SWRL: A Semantic Web Rule Language Combining OWL and RuleML;, 2004; http://www.w3.org/Submission/2004/SUBM-SWRL-20040521/., W3C Member Submission 21 May.
46. Cheung, K; Yip, K. Y.; Smith, A.; deKnikker, R.; Masiar, A.; Gerstein, M. YeastHub: a semantic web use case for integrating data in the life sciences domain Bioinformatics 2005, 21, 85-96
47. Kerrien, S.; Alam-Faruque, Y.; Aranda, B.; Bancarz, I.; Bridge, A.; Derow, C.; Dimmer, E.; Feuermann, M.; Friedrichsen, A.; Huntley, R.; Kohler, C.; Khadake, J.; Leroy, C.; Liban, A.; Lieftink, C.; Montecchi-Palazzi, L.; Orchard, S.; Risse, J.; Robbe, K.; Roechert, B.; Thorneycroft, D.; Zhang, Y.; Apweiler, R.; Hermjakob, H. IntAct-open source resource for molecular interaction data Nucleic Acids Res. 2007, 35 (Database issue) D561-5