An overview of ontologies and data resources in medical domains

Expert Systems with Applications

Volumn 41, Issue 11, 2014, Pages 5158-5166

  Ivanović, Mirjana ^a   Budimac, Zoran ^a  

^a UNIVERSITY OF NOVI SAD   (Serbia)

Author keywords

Biomedical resources and systems; Medical terminologies; Ontologies

Indexed keywords

INFORMATION TECHNOLOGY; INTELLIGENT SYSTEMS; KNOWLEDGE MANAGEMENT; ONTOLOGY; RESEARCH; SEMANTICS; TERMINOLOGY;

AUTOMATED REASONING; BIOMEDICAL RESOURCE; DECLARATIVE KNOWLEDGE; INTERDISCIPLINARY RESEARCH; MEDICAL TERMINOLOGIES; RECENT RESEARCHES; REFERENCE SYSTEMS; STATE OF THE ART;

BIOLOGY;

EID: 84898010725     PISSN: 09574174     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.eswa.2014.02.045     Document Type: Review

References (50)

1. G. Alterovitz, M. Xiang, D. Hill, J. Lomax, J. Liu, and J. Cherkassky et al. Ontology engineering Nature Biotechnology 28 2010 128 130
2. A. Aronson, and F. Lang An overview of MetaMap: Historical perspective and recent advances JAMIA 17 2010 229 236
3. J. Bard, and S. Rhee Ontologies in biology: Design, applications and future challenges Nature Reviews Genetics 5 2004 213 222
4. J. Beilby Diagnostic molecular biology Clinical Biochemist Reviews 27 1 2006 3 4
5. M. Bhatt, W. Rahayu, S. Soni, and C. Wouters Ontology driven semantic profiling and retrieval in medical information systems Web Semantics: Science, Services and Agents on theWorldWideWeb 7 2009 317 331
6. Bo, H., Dupplaw, D., Croitoru, M., Dasmahapatra, S., & Lewis, P. (2007). Facilitating knowledge management in distributed healthcare systems. In The 3rd international conference on semantic technologies. Graz, Austria.
7. O. Bodenreider The unified medical language system (UMLS): Integrating biomedical terminology Nucleic Acids Research 32 2004 D267 D270
8. Bontas, E. (2005). Practical experiences in building ontology-based retrieval systems. In Proceedings of the 1st international ISWC workshop on semantic web case studies and best practices for eBusiness SWCASE05.
9. Clinical, O. (2013, November 1). Methods and tools for representing computerised clinical guidelines. Retrieved from open clinical knowledge management for medical care: < http://www.openclinical.org/gmmsummaries.html >.
10. Corsar, D., Moss, L., Sleeman, D., & Sim, M. (2009). Supporting the development of medical ontologies. In Proceedings of the 4th workshop formal ontologies meet industry 2009 in association with the 10th European conference on knowledge management (pp. 114-125). Vicenza: Frontiers in Artificial Intelligence and Applications 198 IOS Press.
11. FMA. (2012, March 5). Retrieved from foundational model of anatomy: < http://sig.biostr.washington.edu/projects/fm >.
12. F. Freitas, D. Schulz, and E. Moraes Survey of current terminologies and ontologies in biology and medicine RECIIS-Electronic Journal of communication information and Innovation in Health 3 1 March 2009 7 18
13. K.W. Fung, and O. Bodenreider Knowledge representation and ontologies Clinical research informatics, health informatics 2012 Springer-Verlag London Limited Publishing (pp. 255-275)
14. L.M. Garshol Metadata? Thesauri? Taxonomies? Topic maps! making sense of it all Journal of Information Science 30 4 2004 378 391
15. J. Golbeck, G. Fragoso, F. Hartel, J. Hendler, J. Oberthaler, and B. Parsia The national cancer institute's thesaurus and ontology Journal of Web Semantics 1 1 2003 75 80
16. T. Gruber A translation approach to portable ontologies Knowledge Acquisition 5 2 1995 199 220
17. R. Hoehndorf, M. Dumontier, and G.V. Gkoutos Evaluation of research in biomedical ontologies Briefings in Bioinformatics 14 6 2013 696 712
18. ICBOProceedings. (2011). In Proceedings of the 2nd international conference on biomedical ontology. Buffalo, NY, USA.
19. F.T. Imam, S.D. Larson, A. Bandrowski, J.S. Grethe, A. Gupta, and M.E. Martone Development and use of ontologies inside the neuroscience information framework: A practical approach Frontiers in Genetics 3 2012 111
20. C. Jonquet, M. Musen, and N. Shah Building a biomedical ontology recommender web service Journal of Biomedical Semantics 1 Suppl 1 2010 S1
21. S. Kiefer, J. Rauch, R. Albertoni, M. Attene, F. Giannini, and S. Marini et al. The CHRONIOUS ontology-driven search tool: Enabling access to focused and up-to-date healthcare literature C. Paul, C. Miriam, Proceedings of eChallenges e-2011 conference 2011 IIMC International Information Management Corporation
22. W.R. Kubick The semantics of health care interoperability Applied Clinical Trials 18 10 2009
23. Kunierczyk, W. (2006). Nontological engineering formal ontology in information systems. In Proceedings of the 4th international conference FOIS 2006 (pp. 39-50). Amsterdam, The Netherlands: IOS Press.
24. V. Luković, D. Milošević, G. Devedžić, and S. Ćuković Converting OBR-Scolio ontology in OWL DL Computer Science and Information Systems 10 3 2013
25. J.S. McIlwain Data standards harmonization Applied Clinical Trials 19 5 2010 1 6
26. MESH. (2012, March 10). Retrieved from medical subject headings: < http://www.nlm.nih.gov/mesh >.
27. NCI-EVS. (2013, November 6). Retrieved from national cancer institute, enterprise vocabulary services: < http://evs.nci.nih.gov/ >.
28. S.J. Nelson, T. Powell, and L.B. Humphreys The unified medical language system (UMLS) of the national library of medicine Journal of American Medical Record Association 61 2006 40 42
29. S. Nelson, and J. Schulman A multilingual vocabulary project - managing the maintenance environment 2007 MeSH Section, National Library of Medicine Bethesda, Maryland
30. N. Noy, N. Shah, P. Whetzel, B. Dai, M. Dorf, and N. Griffith et al. BioPortal: Ontologies and integrated data resources at the click of a mouse Nucleic Acids Research 37 2009 170 173
31. N. Noy, T. Tudorache, C. Nyulas, and M. Musen The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies AMIA Annual Symposium proceedings 2010 552 556
32. OBO. (2012, March 15). Retrieved from the open biological and biomedical ontologies: < http://www.obofoundry.org >.
33. A. Parker, I. McCaffery, and S. Patterson Examining molecular biology in humans BioTechniques 46 5 2009 358 360
34. Pedro, V., Lita, L., Niculescu, R., Rao, B., & Carbonell, J. (2007). Federated ontology search for the medical domain. OTM workshops, Vol. 1. (pp. 554-565).
35. A. Rector, and S. Brandt Why do it the hard way? The case for an expressive description logic for SNOMED Journal of the American Medical Informatics Association 15 6 2008 744 751
36. A. Rector, S. Brandt, and T. Schneider Getting the foot out of the pelvis: Modeling problems affecting use of SNOMED CT hierarchies in practical applications Journal of the American Medical Informatics Association 18 4 2011 432 440
37. A. Rector, R. Qamar, and T. Marley Binding ontologies and coding systems to electronic health records and messages Journal of Applied Ontology 4 1 2009 51 69
38. P.N. Robinson, and S. Mundlos The human phenotype ontology Clinical Genetics 77 6 2010 525 534
39. C. Rosse, and J. Mejino The foundational model of anatomy ontology A. Burger, D. Davidson, R. Baldock, Anatomy ontologies for bioinformatics: Principles and practice 2007 Springer 59 117
40. D.L. Rubin, S.E. Lewis, C.J. Mungall, S. Misra, M. Westerfield, and M. Ashburner et al. National center for biomedical ontology: Advancing biomedicine through structured organization of scientific knowledge OMICS: A Journal of Integrative Biology 10 2 2006 185 198
41. SemanticHEALTH. (2013, November 6). Retrieved from semantic interoperability deployment and research roadmap, EU IST 6th fw 27328: < http://www.semantichealth.org/ >.
42. B. Smith, M. Ashburner, R. Cornelius, B. Jonathan, B. William, and C. Werner et al. The OBO foundry: Coordinated evolution of ontologies to support biomedical data integration Nature Biotechnology 25 2007 1251 1255
43. B. Smith, and W. Ceusters HL7 RIM: An incoherent standard Studies in Health Technology and Informatics 124 2006 133 138
44. Smith, B., Mejino, J., Schulz, S., & Rosse, C. (2005). Anatomical information science. In COSIT 2005: Spatial Information Theory. Foundations of Geographic Information Science (pp. 149-64). New York: Springer.
45. Spackman, K., Campbell, K., & Côté, R. (1997). SNOMED RT: A reference terminology for health care. In DR. Masys (Ed.), The emergence of internetable health care: Systems that really work. Proceedings of the 1997 AMIA annual symposium (pp. 640-644). Philadelphia: Hanley & Belfus Inc.
46. R. Steinbrook Healthcare and the American recovery and reinvestment act The New England Journal of Medicine 360 2009 1057 1060
47. R. Stevens, P. Baker, S. Bechhofer, G. Ng, A. Jacoby, and N.W. Paton et al. TAMBIS: Transparent access to multiple bioinformatics information sources Bioinformatics 16 2000 184 185
48. UMLS. (2012, March 15). Retrieved from unified medical language system: < http://www.nlm.nih.gov/research/umls/ >.
49. VMW. (2013, November 6). Retrieved from virtual medical worlds: < http://www.hoise.com/vmw/analysis/ >.
50. M. Weiner, and B. Slatko Kits and their unique role in molecular biology: A brief retrospective BioTechniques 44 5 2008 701 704