Towards pharmacogenomics knowledge discovery with the semantic web

Briefings in Bioinformatics

Volumn 10, Issue 2, 2009, Pages 153-163

  Dumontier, Michel ^a   Villanueva Rosales, Natalia ^b  

^a CARLETON UNIVERSITY   (Canada)

^b NONE

Author keywords

Data integration; Ontology design; OWL; Pharmacogenomics; Semantic web; XML

Indexed keywords

AMITRIPTYLINE; ANTIDEPRESSANT AGENT; CITALOPRAM; DESIPRAMINE; FLUOXETINE; MULTIDRUG RESISTANCE PROTEIN 1; NORTRIPTYLINE; VENLAFAXINE;

COMPUTER LANGUAGE; CONFERENCE PAPER; DEPRESSION; GENETIC VARIABILITY; GENOTYPE; HUMAN; INFORMATION DISSEMINATION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; KNOWLEDGE MANAGEMENT; ORTHOSTATIC HYPOTENSION; PATIENT SELECTION; PHARMACOGENOMICS; RECOMMENDED DRUG DOSE; SEMANTICS;

DATABASES, FACTUAL; DEPRESSION; DRUG DESIGN; HUMANS; INFORMATION DISSEMINATION; INFORMATION STORAGE AND RETRIEVAL; INTERNET; KNOWLEDGE BASES; PHARMACOGENETICS; SEMANTICS; SYSTEMS INTEGRATION; TERMINOLOGY AS TOPIC; VOCABULARY, CONTROLLED;

EID: 63349104588     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn056     Document Type: Conference Paper

References (54)

1. Evans WE, Relling MV. Moving towards individualized medicine with pharmacogenomics. Nature 2004;429:464-8.
2. Swen JJ, Huizinga TW, Gelderblom H, et al. Translating pharmacogenomics: Challenges on the road to the clinic. PLoS Med 2007;4:e209.
3. Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, et al. The pharmacogenetics and pharmacogenomics knowledge base: Accentuating the knowledge. Nucleic Acids Res 2008;36: D913-8.
4. Whirl-Carrillo M, Woon M, Thorn CF, et al. An XML-based interchange format for genotype-phenotype data. Hum Mutat 2008; 29:212-9.
5. Mungall CJ, Emmert DB. A Chado case study: An ontology-based modular schema for representing genome-associated biological information. Bioinformatics 2007;23:i337-46.
6. Funahashi A, Jouraku A, Matsuoka Y, et al. Integration of Cell Designer and SABIO-RK. In Silico Biol 2007;7: S81-90.
7. Boulianne L, Al Assaad S, Dumontier M, et al. GridCell: A stochastic particle-based biological system simulator. BMC Syst Biol 2008;2:66.
8. Cline MS, Smoot M, Cerami E, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007;2:2366-82.
9. Berners-Lee T, Hendler J, Lassila O. The Semantic Web, Scientific American, 2001.
10. W3C. OWL Web Ontology Language Guide. http://www.w3.org/TR/ owl-guide/ (last accessed).
11. Horrocks I, Patel-Schneider P, Sattler U, et al. OWL 1.1 Specification. http://owl1_1.cs.manchester.ac.uk/ (last accessed).
12. Sirin E, Parsia B, Grau BC, et al. Pellet: A practical OWL-DL reasoner. Web Semantics 2007;5:51-3.
13. Tsarkov D, Horrocks I. FaCT++ description logic reasoner: System description. In: Joint Conference on Automated Reasoning. London: Springer, 2006, 292-7.
14. Villanueva-Rosales N, Osbahr K, Dumontier M. Towards a semantic knowledge base for yeast biologists. In: First International Workshop on Health Care and Life Sciences Data Integration for the Semantic Web (HCLS 2007). Alberta: Banff, 2007.
15. Ferres L, Dumontier M, Villanueva-Rosales N. Semantic query answering with time-series graphs. In: The 3rd International Workshop on Vocabularies, Ontologies and Rules for The Enterprise (VORTE 2007). USA: Annapolis, 2007.
16. Villanueva-Rosales N, Dumontier M. Describing chemical functional groups in OWL-DL for the classification of chemical compounds. OWL Experiences and Design. Austria: Innsbruck, 2007.
17. Villanueva-Rosales N, Dumontier M. yOWL: An ontology-driven knowledge base for yeast biologists. J Biomed Inform 2008;41(5): 779-89.
18. Parsia B, Patel-Schneider PF. OWL 2 Web Ontology Language: Primer. http://www.w3.org/TR/owl2-primer/ (September 15, 2008, date last accessed).
19. The Gene Ontology project. Nucleic Acids Res 2008;36: D440-4.
20. Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007;25:1251-5.
21. Coulet A, Smail-Tabbone M, Napoli A, et al. Suggested ontology for pharmacogenomics (SO-Pharm): Modular construction and preliminary testing. In: OTM 2006 Proceedings. Berlin/Heidelberg: Springer, 2006; 648-57.
22. Coulet A, Smail-Tabbone M, Benlian P, et al. Ontology-guided data preparation for discovering genotypephenotype relationships. BMC Bioinformatics 2008; 9(Suppl 4):S3.
23. Dumontier M, Faizan M, Obeng J, et al. Modeling the pharmacogenomics of depression. In: Semantic Web for Health Care and Life Sciences Workshop. Beijing: China, 2008.
24. Dumontier M, Villanueva-Rosales N. Three-layer OWL ontology design. Second International Workshop on Modular Ontologies (WOMO07), colocated with Knowledge Capture (KCAP2007). Canada: Whistler, 2007.
25. Pharmacogenomics Ontology Primitive. http://ontology.dumontierlab.com/pharmacogenomics-primitive (August 1, 2008, date last accessed).
26. Rector AL. Modularisation of domain ontologies implemented in description logics and related formalisms including OWL. In: KC2003 Sanibel Island, FL, USA: ACM Press, 2007.
27. Biomedical Measure Ontology. http://ontology.dumontierlab.com/ biomedical-measure-primitive (August 1, 2008 date last accessed).
28. Instantiated Units Ontology. http://ontology.dumontierlab.com/ unit-ontology-individuals (August 1, 2008, date last accessed).
29. PharmGKB XML Schema. http://www.pharmgkb.org/schema/ (August 1, 2008, date last accessed).
30. García R, Gil R. Facilitating business interoperability from the semantic web. In: 10th International Conference on Business Information Systems (BIS) 2007. pp. 220-32.
31. XML Datatype to Object Property and Class Stylesheet. http://ontology.dumontierlab.com/xmldt2owlcop.xsl (August 1, 2008, date last accessed).
32. Grenon P, Smith B, Goldberg L. Biodynamic ontology: Applying BFO in the biomedical domain. Stud Health Technol Inform 2004;102:20-38.
33. Niles I, Pease A. Towards a standard upper ontology. International conference on Formal Ontology in Information Systems. Ogunquit, Maine, USA: ACM, 2001.
34. Herre H, Heller B, Burek P, et al. General Formal Ontology (GFO) - a foundational ontology integrating objects and processes. Onto-Med Report 8, Research Group Ontologies in Medicine, Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany, 2006.
35. Masolo C, Borgo S, Gangem A, et al. Wonder-web deliverable D18: ontology library (final). Tech report, Laboratory for Applied Ontology. Trento, Italy: ISTC-CNR, 2003.
36. Basic Relation Ontology. http://ontology.dumontierlab.com/bro (August 1, 2008, date last accessed).
37. Smith B, Ceusters W, Klagges B, et al. Relations in biomedical ontologies. Genome Biol 2005;6:R46.
38. Pharmacogenomics Ontology Complex. http://ontology.dumontierlab.com/pharmacogenomics-complex (August 1, 2008, date last accessed).
39. NULO Ontology. http://ontology.dumontierlab.com/nulo (August 1, 2008, date last accessed).
40. NULO Constraints. http://ontology.dumontierlab.com/ nulo-constraints (August 1, 2008, date last accessed).
41. BRO + OWL2. http://ontology.dumontierlab.com/broowl2 (August 1, 2008, date last accessed).
42. Pharmacogenomics Knowledge Base with PharmGKB Data. http://ontology.dumontierlab.com/pharmacogenomicspgkb-1.0.owl (August 1, 2008, date last accessed).
43. Pharmacogenomics of Depression Knowledge Base. http://ontology.dumontierlab.com/pharmacogenomics-depression (August 1, 2008, date last accessed).
44. Horridge M, Drummond N, Goodwin J, et al. The Manchester OWL syntax. OWL Experiences and Design. Georgia: Athens, 2006.
45. Systematized Nomenclature of Medicine-Clinical Terms. http://www.ihtsdo.org/snomed-ct/ (August 1, 2008, date last accessed).
46. Konyk M, De Leon A, Dumontier M. Chemical knowledge for the semantic web. In: Bairoch A, Boulakia SC, Froidevaux C, (eds). DILS. Evry, France: Springer, 2008, pp. 169-76.
47. Organic Function Group Ontology. http://ontology.dumontierlab.com/ organic-functional-group-complex (August 1, 2008, date last accessed).
48. Golbreich C, Horridge M, Horrocks I, et al. OBO and OWL: leveraging semantic web technologies for the life sciences. Lect Notes Comput Sci 2007;4825:169.
49. Dumontier M. OWL Ontologies. http://ontology.dumon tierlab.com/ (September 15, 2008, date last accessed).
50. Haarslev V, Möller R, Wessel M. Querying the Semantic Web with Racer + nRQL. In: KI-04 Workshop on Applications on Description Logics, 2004. Ulm.
51. Sirin E, Parsia B. SPARQL-DL: SPARQL query for OWLDL. In: Third OWL Experiences and Directions Workshop (OWLED-2007) 2007.
52. Wishart DS, Knox C, Guo AC, et al. DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008;36 D901-6.
53. Wheeler DL, Barrett T, Benson DA, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008;36:D13-21.
54. The universal protein resource (UniProt). Nucleic Acids Res 2008;36:D190-5.