Biomedical ontologies: A functional perspective

Briefings in Bioinformatics

Volumn 9, Issue 1, 2008, Pages 75-90

  Rubin, Daniel L ^a   Shah, Nigam H ^a   Noy, Natalya F ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Annotation; Data analysis; Ontologies

Indexed keywords

BIOINFORMATICS; BIOMEDICINE; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA ANALYSIS; DECISION SUPPORT SYSTEM; GENETIC DATABASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; MEDICAL INFORMATION SYSTEM; MEDICAL LITERATURE; MEDICAL RESEARCH; MICROARRAY ANALYSIS; ONLINE SYSTEM; PROBABILITY; PROTEIN DATABASE; REVIEW; SCIENTIST; BIOLOGICAL MODEL; BIOLOGY; DOCUMENTATION; FACTUAL DATABASE; LINGUISTICS; METHODOLOGY; NATURAL LANGUAGE PROCESSING; SYSTEM ANALYSIS;

DUDLEYA EDULIS;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DOCUMENTATION; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; NATURAL LANGUAGE PROCESSING; SYSTEMS INTEGRATION; VOCABULARY, CONTROLLED;

EID: 38049144316     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbm059     Document Type: Review

References (59)

1. Hey T, Trefethen AE. Cyberinfrastructure for e-Science. Science 2005;308:817-21.
2. Fedoroff N, Racunas SA, Shrager J. Making biological computing smarter. The Scientist 2005;20-21.
3. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
4. Harris MA, Clark J, Ireland A, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004;32 D258-61.
5. Lewis SE. Gene Ontology: Looking backwards and forwards. Genome Biol 2005;6:103.
6. Drysdale RA, Crosby MA, Gelbart W, et al. FlyBase: Genes and gene models. Nucleic Acids Res 2005;33:D390-5.
7. Sprague J, Clements D, Conlin T, et al. The Zebrafish information Network (ZFIN): The zebrafish model organism database. Nucleic Acids Res 2003;31:241-3.
8. Rhee SY, Dickerson J, Xu D. Bioinformatics and its applications in plant biology. Annu Rev Plant Biol 2006;57: 335-60.
9. Dybkaer R. An ontology on property for physical, chemical, and biological systems. APMIS Suppl 2004;117: 1-210.
10. Huq SZ, Karras BT, A proposed ontology for online healthcare surveys. AMIA Annu Symp Proc 2003;304-9.
11. Ma J. Budding an Ontology-driven database for clinical immune research. AMIA Annu Symp Proc 2006;1018.
12. Sim I, Olasov B, Carini S. An ontology of randomized controlled trials for evidetice-based practice: Content specification and evaluation using the competency decomposition method. J Biomed Inform 2004;37 108-19.
13. Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Methods Inf Med 2006;45(Suppl 1): 124-35.
14. Yu AC. Methods in biomedical ontology. J. Biomed Inform 2006;39 252-66.
15. Bodenreider O, Stevens R. Bio-ontologies: Current trends and future directions. Brief Bioinform 2006;7:256-74.
16. Rojas I, Ratsch E, Saric J, et al. Notes on the use of ontologies in the biochemical domain. In Silico Biol 2004;4: 89-96.
17. Ball CA, Brazma A. MGED standards: Work in progress. Omics 2006; 10:138-44.
18. Rosse C, Mejino JL Jr. A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform 2003;36 478-500.
19. Khatri P, Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005;21:3587-95.
20. Lowe HJ, Barnett GO. Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches. Jama 1994;271:1103-8.
21. Bodenreider O. Using UMLS semantics for classification purposes. Proc AMIA Symp 2000;86-90.
22. Hersh W, Hickam DH, Haynes R-B, et al. Evaluation of SAPHIRE: An automated approach to indexing and retrieving medical literature. Proc Annu Symp Comput Appl Med Care 1991;808-12.
23. Rubin DL, Thorn CF, Klein TE, et al. A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc 2005;12:121-9.
24. Suomela BP, Andrade MA. Ranking the whole MEDLINE database according to a large training set using text indexing, BMC Bioinformatics 2005;6:75.
25. Hartel FW, de Coronado S, Dionne R, et al. Modeling a description logic vocabulary for cancer research. J Biomed Inform 2005;38 114-29.
26. Sioutos N, de Coronado S, Haber MW, et al. NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 2007;40: 30-43.
27. Shah N, Rubin D, Supekar K, et al. Ontology-based annotation and query of Tissue Microarray Data. AMIA Annu Symp Proc 2006;709-13.
28. Langlotz CP. RadLex: A new method for indexing online educational materials. Radiographics 2006;26:1595-7.
29. Martone ME, Gupta A, Ellisman MH. E-neuroscience: Challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci 2004;7:467-72.
30. Horrocks I. An ontology language for the semantic Web, IEEE Intell Syst 2002;17:74-5.
31. BioPax-Consortium. BioPAX: Biological, Pathways Exchange. http://www.biopax.org/ (Dec 2006, date last accessed).
32. Kanehisa M, Goto S, Hattori M, et al. From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res 2006;34 D354-7.
33. Karp PD, Ouzounis CA, Moore-Kochlacs C, et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005;33: 6083-9.
34. Joshi-Tope G, Gillespie M, Vastrik I, et al. Reactome: A knowledgebase of biological pathways. Nucleic Acids Res 2005;33 D428-32.
35. Demir E, Babur O, Dogrusoz U, et al. PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 2002;18: 996-1003.
36. Shannon P, Markiel A, Ozier O, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504.
37. Stevens R, Baker P, Bechhofer S, et al. TAMBIS: Transparent access to multiple bioinformatics information sources. Bioinformatics 2000;16:184-5.
38. Gupta A, Ludascher B, Grethe JS, et al. Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Netw 2003;16:1277-92.
39. Li C, Maryann M, Amarnath G, et al. OntoQuest: Exploring ontological data made easy. Proceedings of the 32nd international conference on Very large data bases - Volume; 32. Seoul, Korea: VLDB Endowment, 2006.
40. Muller HM, Kenny EE, Sternberg PW. Textpresso: An ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2004;2:e309.
41. Rzhetsky A, Koike T, Kalachikov S, et al. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics 2000;16:1120-8.
42. Rodriguez-Esteban R, Iossifov I, Rzhetsky A. Imitating manual curation of text-mined facts in biomedicine. PLoS Comput Biol 2006;2 e118.
43. Brinkley JF. Structural informatics and its applications in medicine and biology. Acad Med 1991;66:589-91.
44. Rosse C, Mejino JL, Modayur BR, et al. Motivation and organizational principles for anatomical knowledge representation: The digital anatomist symbolic knowledge base. J Am Med Inform Assoc 1998;5:17-40.
45. Rubin DL, Dameron O, Bashir Y, et al. Using ontologies linked with geometric models to reason about penetrating injuries. Artif Intell Med 2006;37:167-76.
46. Gifford DK. Blazing pathways through genetic mountains. Science 2001;293:2049-51.
47. Kuchinsky A, Graham K, Moh D, et al. Biological storytelling: A software tool for biological information organization based upon narrative structure. Advanced Visual Interfaces. New York: ACM, 2002.
48. Karp PD. Pathway databases: A case study in computational symbolic theories. Science 2001;293:2040-4.
49. Racunas SA, Shah NH, Albert I, et al. HyBrow: A prototype system for computer-aided hypothesis evaluation. Bioinformatics 2004; 20:i257-64.
50. Racunas SA, Shah N, Fedoroff NV. A Contradiction-based framework for testing gene regulation hypotheses. IEEE Bioinformatics. Palo Alto, California: IEEE Computer Society, Stanford University, 2003.
51. Proteome. Yeast Proteome Database. http://www.proteome.com/YPDhome.html (14 April 2002, date last accessed).
52. Rubin DL, Dameron O, Musen MA. Use of description logic classification to reason about consequences of penetrating injuries. AMIA Annu Symp Proc 2005;649-53.
53. Goldstein MK, Hoffman BB, Coleman RW, et al. Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. Proc AMIA Symp 2000;300-4.
54. Cote RG, Jones P, Apweiler R, et al. The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006;7:97.
55. Rubin DL, Lewis SE, Mungall CJ, et al. National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge. Omics 2006;10:185-98.
56. Noy NF. Semantic-integration: A survey of ontology-based approaches. Sigmod Record 2004;33:65-70.
57. Euzenat J, Mochol M, Shvaiko P, et al. Results of the ontology alignment evaluation initiative 2006. In: Shvaiko P, Euzenat J, Noy -N, et al, (eds). Proc. 1st ISWC 2006 International Workshop on Ontology Matching. Trento, IT: Universita degli Studi di Trento.
58. Noy NF, Guha RV, Musen MA. User ratings of ontologies: Who will rate the raters? Proceedings of the AAAI 2005 Spring Symposium on Knowledge Collection from Volunteer Contributors. Trento, IT: Universita degli Studi di Trento, 2005 Available at: http://www.stanford.edu/~natalya/ papers/SS505NoyN.pdf.
59. Noy NF, Rubin DL, Musen MA. Making biomedical ontologies and ontology repositories work. IEEE Intell Syst 2004;19:78-81.