Bridging the gap between medical and bioinformatics: An ontological case study in colon carcinoma

Computers in Biology and Medicine

Volumn 36, Issue 7-8, 2006, Pages 694-711

  Kumar, Anand ^a   Yip, Yum Lina ^b   Smith, Barry ^a,c   Grenon, Pierre ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; DRUG PRODUCTS; GENETIC ENGINEERING; MEDICAL COMPUTING; PATIENT TREATMENT; ROBUSTNESS (CONTROL SYSTEMS); TUMORS;

BIOLOGICAL INFORMATION; MULTI-GRANULAR DATASOURCE; ONTOLOGICAL PRINCIPLES; TUMOR MARKERS;

COMPUTER SCIENCE;

TUMOR MARKER;

ARTICLE; BIOINFORMATICS; COLON CARCINOMA; HUMAN; MEDICAL INFORMATICS; MEDICAL LITERATURE; MEDICAL RESEARCH; PRIORITY JOURNAL;

COLONIC NEOPLASMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; HUMANS; MEDICAL INFORMATICS; MODELS, ANATOMIC;

EID: 33646840261     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2005.07.001     Document Type: Article

References (33)

1. Martin-Sanchez F., Iakovidis I., Norager S., Maojo V., de Groen P., Van der Lei J., Jones T., Abraham-Fuchs K., Apweiler R., Babic A., Baud R., Breton V., Cinquin P., Doupi P., Dugas M., Eils R., Engelbrecht R., Ghazal P., Jehenson P., Kulikowski C., Lampe K., De Moor G., Orphanoudakis S., Rossing N., Sarachan B., Sousa A., Spekowius G., Thireos G., Zahlmann G., Zvarova J., Hermosilla I., and Vicente F.J. Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. J. Biomed. Inform. 37 1 (2004) 30-42
2. Maojo V., and Kulikowski C.A. Bioinformatics and medical informatics: collaborations on the road to genomic medicine?. J. Am. Med. Inform. Assoc. 10 6 (2003) 515-522
3. Grant A.M., Moshyk A.M., Kushniruk A., and Moehr J.R. Reflections on an arranged marriage between bioinformatics and health informatics. Methods Inf. Med. 42 2 (2003) 116-120
4. Wiemer J., Schubert F., Granzow M., Ragg T., Fieres J., Mattes J., and Eils R. Informatics united: exemplary studies combining medical informatics, neuroinformatics and bioinformatics. Methods Inf. Med. 42 2 (2003) 126-133
5. Martin-Sanchez F., Maojo V., and Lopez-Campos G. Integrating genomics into health information systems. Methods Inf. Med. 41 1 (2002) 25-30
6. Kohane I.S. Bioinformatics and clinical informatics: the imperative to collaborate. J. Am. Med. Inform. Assoc. 7 5 (2000) 512-516
7. Altman R.B. The interactions between clinical informatics and bioinformatics: a case study. J. Am. Med. Inform. Assoc. 7 5 (2000) 439-443
8. Spackman K.A. SNOMED-CT milestones: endorsements are added to already-impressive standards credentials. Health Inform. 21 9 (2004) 54, 56
9. Rosse C., and Mejino J.L.V. A reference ontology for bioinformatics: the foundational model of anatomy. J. Biomed. Inform. 36 (2003) 478-500
10. The Gene Ontology Consortium. The gene ontology (GO) database and informatics resource. Nucleic Acids Res. 32 (2004) D258-D261
11. Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., and Yeh L.S. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32 (2004) D115-D119
12. Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, and National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 2000. World Wide Web URL: (http://www.ncbi.nlm.nih.gov/omim/)
13. A. Kumar, B. Smith, Towards a proteomics metaclassification, IEEE Fourth Symposium on Bioinformatics and Bioengineering, Taichung, Taiwan. IEEE Press, New York, 2004, pp. 419-427.
14. B. Smith, J. Koehler, A. Kumar, On the application of formal principles to life science data: a case study in the gene ontology, in: DILS 2004, Leipzig, Lecture Notes in Bioinformatics, vol. 2994, 2004, pp.79-94.
15. A. Kumar, B. Smith, The Unified Medical Language System and the Gene Ontology: Some Critical Reflections, Lecture Notes in Computer Science, vol. 2821/2003, 2003, pp. 135-148.
16. B. Smith, J. Williams, S. Schulze-Kremer, The ontology of the gene ontology, in: Proceedings of the AMIA, 2003, pp. 609-613.
17. O. Bodenreider, B. Smith, A. Kumar, A. Burgun, Investigating subsumption in DL-based terminologies: a case study in SNOMED CT. KR-MED, 2004, in press.
18. DeVita V.T., Hellman S., and Rosenberg S.A. Cancer: Principles and Practice of Oncology. sixth ed. (2001), Lippincott, Williams & Wilkins, Philadelphia, PA, Baltimore, MD
19. Braunwald E., Fauci A.S., Kaspere D.L., Hauser S.L., Longo D.L., and James J.L. Harrison's Principles of Internal Medicine. 15th ed. (2001), McGraw-Hill Professional Publishing, New York
20. Yip Y.L., Scheib H., Diemand A.V., Gattiker A., Famiglietti L.M., Gasteiger E., and Bairoch A. The Swiss-Prot variant page and the ModSNP database. Hum Mutat. 23 5 (2004) 464-470
21. Camon E., Magrane M., Barrell D., Lee V., Dimmer E., Maslen J., Binns D., Harte N., Lopez R., and Apweiler R. The gene ontology annotation (GOA) database: sharing knowledge in uniprot with gene ontology. Nucleic Acids Res. 32 (2004) D262-D266
22. Agrawal R., and Srikant R. Fast algorithms for mining association rules in large databases. Proceedings of the International Conference on Very Large Databases (1994), Santiage, Chile, Morgan Kaufmann, Los Altos, CA 478-499
23. C. Masolo, S. Borgo, A. Gangemi, N. Guarino, A. Oltramari, Ontology Library (final), WonderWeb deliverable D18, December 2003.
24. Grenon P., and Smith B. SNAP and SPAN: towards dynamic spatial ontology. Spatial Cognition and Computation 4 1 (2004) forthcoming
25. B. Smith, P. Grenon, The Cornucopia of Formal-Ontological Relations, Dialectica, 58(3) (2004), 279-296.
26. Anon. TNM system. J. Am. College Surg. 181 (1995) 182-188
27. Yarbro J.W., Page D.L., Fielding L.P., et al. American joint committee on cancer prognostic factors consensus conference. Cancer 86 11 (1999) 2436-2446
28. Han K., Park B., Kim H., Hong J., and Park J. HPID: the human protein interaction database. Bioinformatics 20 15 (2004) 2466-2470
29. Hermjakob H., Montecchi-Palazzi L., Lewington C., Mudali S., Kerrien S., Orchard S., Vingron M., Roechert B., Roepstorff P., Valencia A., Margalit H., Armstrong J., Bairoch A., Cesareni G., Sherman D., and Apweiler R. IntAct: an open source molecular interaction database. Nucleic Acids Res. 32 (2004) D452-D455
30. Fleischmann A., Darsow M., Degtyarenko K., Fleischmann W., Boyce S., Axelsen K.B., Bairoch A., Schomburg D., Tipton K.F., and Apweiler R. IntEnz, the integrated relational enzyme database. Nucleic Acids Res. 32 (2004) D434-D437
31. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., and Eisenberg D. The database of interacting proteins: 2004 update. Nucleic Acids Res. 32 (2004) D449-D451
32. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
33. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242