The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside

Journal of Biomedical Semantics

Volumn 2, Issue 2, 2011, Pages

  Luciano, Joanne S ^a,b   Andersson, Bosse ^c   Batchelor, Colin ^d   Bodenreider, Olivier ^e   Clark, Tim ^f,g   Denney, Christine K ^h   Domarew, Christopher ⁱ   Gambet, Thomas ^j   Harland, Lee ^k   Jentzsch, Anja ^l   Kashyap, Vipul ^m   Kos, Peter ^f   Kozlovsky, Julia ⁿ   Lebo, Timothy ^a   Marshall, Scott M ^o,p   McCusker, James P ^a   McGuinness, Deborah L ^a   Ogbuji, Chimezie ^q   Pichler, Elgar ^r   Powers, Robert L ^b   Prud'hommeaux, Eric ^j   Samwald, Matthias ^s,t,u   Schriml, Lynn ^v   Tonellato, Peter J ^f   Whetzel, Patricia L ^w   Zhao, Jun ^x   Stephens, Susie ^y   Dumontier, Michel ^z   more..

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b Predictive Medicine   (United States)

^c ASTRAZENECA R AND D   (Sweden)

^d ROYAL SOCIETY OF CHEMISTRY   (United Kingdom)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

^g UNIVERSITY OF MANCHESTER   (United Kingdom)

^h ELI LILLY AND COMPANY   (United States)

ⁱ ALBANY MEDICAL CENTER   (United States)

^j W3C   (United States)

^k PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^l FREIE UNIVERSITÄT BERLIN   (Germany)

^m CIGNA HealthCare   (United States)

ⁿ ASTRAZENECA   (United Kingdom)

^o LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^p UNIVERSITY OF AMSTERDAM   (Netherlands)

^q CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^r Medical University of Vienna ^*  (United States)

^s MEDICAL UNIVERSITY OF VIENNA   (Austria)

^t Information Retrieval Facility   (Austria)

^u NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^v UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^w STANFORD UNIVERSITY   (United States)

^x UNIVERSITY OF OXFORD   (United Kingdom)

^y Johnson and Johnson Pharmaceutical Research and Development   (United States)

^z CARLETON UNIVERSITY   (Canada)

more..

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872872194     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-2-S2-S1     Document Type: Article

References (61)

1. Trusheim M, Berndt E, Douglas F: Stratified medicine: strategic and economic implications of combining drugs and clinical biomarkers. Nature Reviews Drug Discovery. 2007, 6 (4): 287-293. 10.1038/nrd2251.
2. Woolf S: The meaning of translational research and why it matters. JAMA. 2008, 299 (2): 211-10.1001/jama.2007.26.
3. Rodwin M: The case for public ownership of patient data. JAMA. 2009, 302: 86-10.1001/jama.2009.965.
4. Roses A: Pharmacogenetics in drug discovery and development: a translational perspective. Nature Reviews Drug Discovery. 2008, 7 (10): 807-817. 10.1038/nrd2593.
5. Centers for Medicare & Medicaid Services (CMS): Medicare & Medicaid EHR Incentive Program Meaningful Use Web Site. [ http://www.cms.gov/EHRIncentivePrograms/35_Meaningful_Use.asp ]
6. Office of the National Coordinator for Health Information Technology (ONCHIT): Standards & Certification Criteria Web Site. [ http://healthit.hhs.gov/portal/server.pt/community/healthit/hhs/gov/standards/ifr/1195 ]
7. Luciano JS, Negishi M, Cohen MA, Samson JA: Depression Research: Modeling to Illuminate Darkness. Neural Modeling of Cognitive and Brain Disorders. Edited by: Reggia J, Ruppin E, Berndt R. 1996, World Scientific Publishing Company
8. Luciano JS: Neural Network Modeling of Unipolar Depression: Patterns of Recovery and Prediction of Outcome. PhD thesis. 1996, Boston University
9. Levine M, Calvanio R: The Recording of Personal Information as an Intervention and as an Electronic Health Support. 2007, Springer
10. Calvanio R, Buonanno F, Levine D, Levine M: Neuropsychiatric sequelae and life events: Analysis and management. 6th World Stroke Congress. 2008
11. Health Care and Life Sciences Pathology Radiology Correlation. [ http://esw.w3.org/HCLSIG/Terminology/PathRadCorrelation ]
12. Allemang D, Hendler J: Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL. 2008, Morgan Kaufmann
13. Deus H, Zhao J, Sahoo S, Samwald M, Prud'hommeaux E, Miller M, Marshall M, Cheung KH: Provenance of Microarray Experiments for a Better Understanding of Experiment Results. Proceedings of The Second International Workshop on the role of Semantic Web in Provenance Management. 2010, Shanghai, China
14. McGuinness D, Pinheiro da Silva P: Explaining answers from the semantic web: The inference web approach. Web Semantics: Science, Services and Agents on the World Wide Web. 2004, 1 (4): 397-413. 10.1016/j.websem.2004.06.002.
15. Dumontier M, Villanueva-Rosales N: Towards pharmacogenomics knowledge discovery with the semantic web. Briefings in Bioinformatics. 2009, 10 (2): 153-10.1093/bib/bbn056.
16. Coulet A, Smail-Tabbone M, Napoli A, Devignes M: Suggested Ontology For Pharmacogenomics (SO-Pharm): Modular Construction And Preliminary Testing. Lecture Notes in Computer Science. 2006, 4277: 648-657. full_text.
17. Arikuma T, Yoshikawa S, Azuma R, Watanabe K, Matsumura K, Konagaya A: Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation. BMC Bioinformatics. 2008, 9 (Suppl 6): S11-10.1186/1471-2105-9-S6-S11.
18. Luciano JS: PAX of mind for pathway researchers. Drug Discovery Today. 2005, 10 (13): 937-942. 10.1016/S1359-6446(05)03501-4.
19. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KHH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD: The BioPAX community standard for pathway data sharing. Nature biotechnology. 2010, 28 (9): 935-942. 10.1038/nbt.1666.
20. Shah N, Jonquet C, Chiang A, Butte A, Chen R, Musen M: Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009, 10 (Suppl 2): S1-10.1186/1471-2105-10-S2-S1.
21. Jentzsch A, Zhao J, Hassanzadeh O, Cheung K, Samwald M, Andersson B: Linking open drug data. Triplification Challenge of the International Conference on Semantic Systems. 2009, Citeseer
22. Patterson C, Feightner J, Garcia A, Hsiung G, MacKnight C, Sadovnick A: Diagnosis and treatment of dementia: 1. Risk assessment and primary prevention of Alzheimer disease. Canadian Medical Association Journal. 2008, 178 (5): 548-10.1503/cmaj.070796.
23. Minati L, Edginton T, Grazia Bruzzone M, Giaccone G: Reviews: Current Concepts in Alzheimer's Disease: A Multidisciplinary Review. American Journal of Alzheimer's Disease and Other Dementias. 2009, 24 (2): 95-10.1177/1533317508328602.
24. Jack C, Wiste H, Vemuri P, Weigand S, Senjem M, Zeng G, Bernstein M, Gunter J, Pankratz V, Aisen P: Brain beta-amyloid measures and magnetic resonance imaging atrophy both predict time-to-progression from mild cognitive impairment to Alzheimer's disease. Brain. 2010, 133 (11): 3336-10.1093/brain/awq277.
25. Kolate G: Sharing of Data Leads to Progress on Alzheimer's. New York Times. 2010, [ Http://www.nytimes.com/2010/08/13/health/research/13alzheimer.html ]
26. HCLS Translational Medicine Task Force. [ http://www.w3.org/wiki/HCLSIG/PharmaOntology ]
27. Scheuermann R, Ceusters W, Smith B: Toward an ontological treatment of disease and diagnosis. Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. 2009, 116-120.
28. Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C: Relations in biomedical ontologies. Genome Biology. 2005, 6 (5): R46-10.1186/gb-2005-6-5-r46.
29. Noy N, Shah N, Whetzel P, Dai B, Dorf M, Griffith N, Jonquet C, Rubin D, Storey M, Chute C, Musen M: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009, 1: 37-
30. UMLS: [ http://www.nlm.nih.gov/research/umls/ ]
31. Dubois B, Feldman H, Jacova C, DeKosky S, Barberger-Gateau P, Cummings J, Delacourte A, Galasko D, Gauthier S, Jicha G: Research criteria for the diagnosis of Alzheimer's disease: revising the NINCDS-ADRDA criteria. The Lancet Neurology. 2007, 6 (8): 734-746. 10.1016/S1474-4422(07)70178-3.
32. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo A, Wishart D: DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011, D1035-41. 10.1093/nar/gkq1126. Database Issue
33. Thorn C, Klein T, Altman R: Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics. 2010, 4: 501-5. 10.2217/pgs.10.15.
34. Belleau F, Nolin M, Tourigny N, Rigault P, Morissette J: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics. 2008, 41 (5): 706-716. 10.1016/j.jbi.2008.03.004.
35. The Indivo Personally Controlled Health Record. [ http://indivohealth.org ]
36. Hassanzadeh O, Kementsietsidis A, Lim L, Miller R, Wang M: A framework for semantic link discovery over relational data. Proceedings of the 18th ACM Conference on Information and Knowledge Management. 2009, ACM, 1027-1036. full_text.
37. Volz J, Bizer C, Gaedke M, Kobilarov G: Silk-a link discovery framework for the web of data. Proceedings of the 2nd Linked Data on the Web Workshop. 2009
38. Stephens S, LaVigna D, DiLascio M, Luciano J: Aggregation of bioinformatics data using Semantic Web technology. Web Semant. 2006, 4: 216-221. 10.1016/j.websem.2006.05.004. [ http://portal.acm.org/citation.cfm?id=1222219.1222307 ]
39. Weitzner D, Abelson H, Berners-Lee T, Hanson C, Hendler J, Kagal L, McGuinness D, Sussman G, Waterman K: Transparent accountable inferencing for privacy risk management. AAAI Spring Symposium on The Semantic Web meets eGovernment. 2006, AAAI Press, Stanford University, USA, Citeseer
40. Zerhouni E: Translational and clinical science-time for a new vision. New England Journal of Medicine. 2005, 353 (15): 1621-10.1056/NEJMsb053723.
41. Mirhaji P, Zhu M, Vagnoni M, Bernstam E, Zhang J, Smith J: Ontology driven integration platform for clinical and translational research. BMC bioinformatics. 2009, 10 (Suppl 2): S2-10.1186/1471-2105-10-S2-S2.
42. Kamel N, Compton C, Middelveld R, Higenbottam T, Dahlén S: The Innovative Medicines Initiative (IMI): a new opportunity for scientific collaboration between academia and industry at the European level. European Respiratory Journal. 2008, 31 (5): 924-10.1183/09031936.00033208.
43. 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 M, Ogbuji C, Rees J, Stephens S, Wong G, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung K: Advancing translational research with the Semantic Web. BMC Bioinformatics. 2007, 8 (Suppl 3): S2-10.1186/1471-2105-8-S3-S2.
44. Kashyap V, Hongsermeier T: Can semantic web technologies enable translational medicine?. Semantic Web. 2007, 249-279.
45. Biomedical Research Integrated Domain Group. [ http://www.bridgmodel.org ]
46. Sioutos N, Coronado S, Haber M, Hartel F, Shaiu W, Wright L: NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics. 2007, 40: 30-43. 10.1016/j.jbi.2006.02.013.
47. Stearns M, Price C, Spackman K, Wang A: SNOMED clinical terms: overview of the development process and project status. Proceedings of the AMIA Symposium. 2001, American Medical Informatics Association, 662-
48. Murphy S, Weber G, Mendis M, Gainer V, Chueh H, Churchill S, Kohane I: Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). Journal of the American Medical Informatics Association. 2010, 17 (2): 124-10.1136/jamia.2009.000893.
49. Luciano J, Stevens R: e-Science and biological pathway semantics. BMC Bioinformatics. 2007, 8 (Suppl 3): S3-10.1186/1471-2105-8-S3-S3.
50. Hey T, Trefethen A: Cyberinfrastructure for e-Science. Science. 2005, 308 (5723): 817-821. 10.1126/science.1110410.
51. Hey T, Trefethen A: e-Science and its implications. Philos Transact A Math Phys Eng Sci. 2003, 361 (1809): 1809-1825. 10.1098/rsta.2003.1224.
52. McGuinness D, Ding L, da Silva P, Chang C: Pml 2: A modular explanation interlingua. Proceedings of AAAI. 2007, 7:
53. Moreau L, Clifford B, Freire J, Futrelle J, Gil Y, Groth P, Kwasnikowska N, Miles S, Missier P, Myers J: The open provenance model core specification (v1. 1). Future Generation Computer Systems. 2010
54. Sahoo S, Bodenreider O, Hitzler P, Sheth A, Thirunarayan K: Provenance Context Entity (PaCE): Scalable provenance tracking for scientific RDF data. Proceedings of the 22nd International Scientific and Statistical Database Management (SSDBM) Conference. 2010, SSDBM, 461-470.
55. McGuinness D, Fox P, Brodaric B, Kendall E: The Emerging Field of Semantic Scientific Knowledge Integration. IEEE Intelligent Systems. 2009, 25-26.
56. Tao J, Ding L, McGuinness D: Instance data evaluation for semantic web-based knowledge management systems. System Sciences, 2009. HICSS'09. 42nd Hawaii International Conference on. 2009, IEEE, 1-10.
57. Halpin H, Hayes P, McCusker J, McGuinness D, Thompson H: When owl: sameAs isn't the Same: An Analysis of Identity in Linked Data. Proc. 9th Int. Semantic Web Conf. 2010
58. Ding L, Shinavier J, Shangguan Z, McGuinness D: SameAs Networks and Beyond: Analyzing Deployment Status and Implications of owl: sameAs in Linked Data. Proc. 9th Int. Semantic Web Conf. 2010
59. Goble C, Pettifer S, Stevens R, Greenhalgh C: Knowledge Integration: In Silico Experiments in Bioinformatics. The Grid: Blueprint for a New Computing Infrastructure. 2003, 121-134.
60. Semantic Publishing and Referencing. [ http://esw.w3.org/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20101115 ]
61. Semantically Annotated LaTeX for scientific publications. [ http://www.springerlink.com/content/t220214924577133/ ]