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2015, Number 1

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Revista Cubana de Informática Médica 2015; 7 (1)

Terminologies and classification systems in Biomedical Sciences

Castrillón-Betancur JC, Flórez-Arango JF

Language: English
References: 59
Page: 89-104
PDF size: 174.45 Kb.


ABSTRACT

Standards terminologies emerged as an attempt to reduce the diversity terminology in scientific languages, facilitating good communication, which is the basis of all scientific research. This review explains principles and applications associated with terminologies and classification systems focusing mainly on the field of biomedical sciences. The research was conducted on scientific databases, books and network using the keywords: Terminologies, Classification systems, Medical Informatics, Electronic Health Records systems, Interoperability, Ontologies and Bio-ontologies. This review is intended to explain that terminologies facilitate good communication, reducing terminology diversity and they are not static systems. They can "evolve" to more complex structures like biomedical ontologies, with the aim of being used with multiple purposes beginning with the efficient transfer of information, to the processing of information as a result of biological research for its understanding.


REFERENCES

  1. Runciman W, Hibbert P, Thomson R, Van Der Schaaf T, Sherman H, Lewalle P. Towards an International Classification for Patient Safety: key concepts and terms. Int J Qual Health Care. 2009 Feb [cited 2014 April 15];21(1):18-26. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/19147597

  2. Chute CG. Clinical classification and terminology: some history and current observations. J Am Med Inform Assoc. 2000 May-Jun [cited 2014 April 15];7(3):298-303. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC61433/

  3. Lathrop SL, Davis WL, Nolte KB. Medical terminology coding systems and medicolegal death investigation data: searching for a standardized method of electronic coding at a statewide medical examiner's office. J Forensic Sci. 2009 Jan [cited 2014 April 10];54(1):207-11. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/19018939

  4. Hardiker NR, Hoy D, Casey A. Standards for nursing terminology. J Am Med Inform Assoc. 2000 Nov-Dec [cited 2014 April 10];7(6):523-8. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/11062225

  5. Barra DC, Sasso GT. Data standards, terminology and classification systems for caring in health and nursing. Rev Bras Enferm. 2011 Nov-Dec [cited 2014 April 12];64(6):1141-9. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/22664615

  6. Kahn MG, Bailey LC, Forrest CB, Padula MA, Hirschfeld S. Building a common pediatric research terminology for accelerating child health research. Pediatrics. 2014 Mar [cited 2014 April 10];133(3):516-25. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/24534404

  7. Dias CA. Terminologia: conceitos e aplicações. Ci Inf. 2000 [cited 2014 April 10];29(1):90-2. Avalaible in: http://revista.ibict.br/ciinf/index.php/ciinf/article/view/270/238

  8. Rosenbloom ST, Miller RA, Johnson KB, Elkin PL, Brown SH. Interface terminologies: facilitating direct entry of clinical data into electronic health record systems. J Am Med Inform Assoc. 2006 May-Jun [cited 2014 April 15];13(3):277-88. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513664/

  9. Evans DA, Cimino JJ, Hersh WR, Huff SM, Bell DS. Toward a medical-concept representation language. The Canon Group. J Am Med Inform Assoc. 1994 May-Jun [cited 2014 April 15];1(3):207-17. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/7719804

  10. Campbell KE, Oliver DE, Spackman KA, Shortliffe EH. Representing thoughts, words, and things in the UMLS. J Am Med Inform Assoc. 1998 Sep-Oct [cited 2014 April 15];5(5):421-31. Avalaible in: http://jamia.oxfordjournals.org/content/5/5/421.long

  11. Shortliffe EH, Cimino JJ. Biomedical informatics: computer applications in health care and biomedicine. 3rd ed. New York, NY: Springer; 2006.

  12. Johnson SB, Clayton PD. Designing an introspective, multipurpose, controlled medical vocabulary. Proceedings of the American Medical Informatics Association. [Conference Paper]. 1989;513-8.

  13. Coiera E. Guide to health informatics. 2nd ed. London New York, NY: Arnold; Distributed in the USA by Oxford University Press; 2003.

  14. Giannangelo K. Healthcare code sets, clinical terminologies, and classification systems. 2nd ed. Chicago: American Health Information Management Association; 2010.

  15. Willett TG, Marshall KC, Broudo M, Clarke M. It's about TIME: a general-purpose taxonomy of subjects in medical education. Med Educ. 2008 Apr [cited 2014 April 10];42(4):432-8. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/18298447

  16. Blaum WE, Jarczweski A, Balzer F, Stotzner P, Ahlers O. Towards Web 3.0: taxonomies and ontologies for medical education -- a systematic review. GMS Z Med Ausbild. 2013 [cited 2014 April 10];30(1):Doc13. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/23467484

  17. Harris ST, Zeng X, Ross T, Ford L. International classification of diseases, 10th revision training: what coders are saying. Health Care Manag (Frederick). 2014 Jan-Mar [cited 2014 April 20];33(1):91-3. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/24463596

  18. Stenzhorn H, Schulz S, Boeker M, Smith B. Adapting Clinical Ontologies in Real-World Environments. J Univers Comput Sci. 2008 [cited 2014 April 20];14(22):3767-80. Avalaible in: http://jucs.org/jucs_14_22/adapting_clinical_ontologies_in/jucs_14_22_3767_3780_stenzhorn.pdf

  19. De Lusignan S, Chan T, Jones S. Large complex terminologies: more coding choice, but harder to find data--reflections on introduction of SNOMED CT (Systematized Nomenclature of Medicine--Clinical Terms) as an NHS standard. Inform Prim Care. 2011 [cited 2014 April 20];19(1):3-5. Avalaible in: http://www.researchgate.net/profile/Simon_De_Lusignan2/publication/51835332_Large_complex_terminologies_more_coding_choice_but_harder_to_find_data--reflections_on_introduction_of_SNOMED_CT_%28Systematized_Nomenclature_of_Medicine--Clinical_Terms%29_as_an_NHS_standard/links/0c96051563bcc61992000000.pdf

  20. Cornet R, de Keizer N. Forty years of SNOMED: a literature review. BMC Med Inform Decis Mak. 2008 [cited 2014 April 20];8 Suppl 1:S2. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582789/

  21. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May [cited 2014 April 23];25(1):25-9. Avalaible in: http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html

  22. Magka D, Krotzsch M, Horrocks I. A rule-based ontological framework for the classification of molecules. J Biomed Semantics. 2014 Apr 15 [cited 2014 April 23];5(1):17. Avalaible in: http://www.jbiomedsem.com/content/5/1/17

  23. Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, et al. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim Biophys Acta. 2014 Jan [cited 2014 April 23];1844(1 Pt A):98-107. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898906/

  24. Cimino JJ. Desiderata for controlled medical vocabularies in the twenty-first century. Methods Inf Med. 1998 Nov [cited 2014 April 23];37(4-5):394-403. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415631/

  25. Legg M. Standardisation of test requesting and reporting for the electronic health record. Clin Chim Acta. 2013 Dec 13 [cited 2014 April 15]. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/24333615

  26. World Health Organization WHO [página web en internet]. Classification of Diseases (ICD). Ginebra: International Classification of Diseases (ICD). 2014 [cited 2014 April 15]. Avalaible in: http://www.who.int/classifications/icd/en/

  27. Hirsch JA, Leslie-Mazwi TM, Nicola GN, Barr RM, Bello JA, Donovan WD, et al. Current procedural terminology; a primer. J Neurointerv Surg. 2014 Mar 3 [cited 2014 April 15]. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/24589819

  28. Americam Medical Associaton AMA [página web en internet]. CPT - Current Procedural Terminology. Chicago: Current Procedural Terminology (CPT). 2014 [cited 2014 April 15]. Avalaible in: http://www.ama-assn.org/ama/pub/physician-resources/solutions-managing-your-practice/coding-billing-insurance/cpt.page

  29. Alexander S, Conner T, Slaughter T. Overview of inpatient coding. Am J Health Syst Pharm. 2003 Nov 1 [cited 2014 April 15];60 (21) Suppl 6:S11-4. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/14619128

  30. Centers for Medicare Services CMS [página web en internet]. HCPCS - General Information. Baltimore: Healthcare Common Procedure Coding System (HCPCS). 2014 [cited 2014 April 15]. Avalaible in: http://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo/index.html?redirect=/MedHCPCSGeninfo/

  31. Food and Drug Adminstration FDA [página web en internet]. National Drug Code Directory. Silver Spring: National Drug Codes (NDCs) 2014 [cited 2014 April 15]. Avalaible in: http://www.fda.gov/drugs/informationondrugs/ucm142438.htm

  32. Simonaitis L, McDonald CJ. Using National Drug Codes and drug knowledge bases to organize prescription records from multiple sources. Am J Health Syst Pharm. 2009 Oct 1 [cited 2014 April 15];66(19):1743-53. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/19767382

  33. Wang YC, Chen SL, Deng NY, Wang Y. Network predicting drug's anatomical therapeutic chemical code. Bioinformatics. 2013 May 15 [cited 2014 April 15];29(10):1317-24. Avalaible in: http://bioinformatics.oxfordjournals.org/content/29/10/1317.long

  34. World Health Organization WHO [página web en internet]. Structure and principles. Ginebra: Anatomical Therapeutic Chemical (ATC). 2014 [cited 2014 April 15]. Avalaible in: http://www.whocc.no/atc/structure_and_principles/

  35. Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Yearb Med Inform. 2006 [cited 2014 April 15]:124-35. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/17051306

  36. Logical Observation Identifiers Names and Codes (LOINC) [página web en internet]. A universal code system for tests, measurements, and observations. Indianápolis. 2014 [cited 2014 April 15]. Avalaible in: http://loinc.org/

  37. Bakken S, Cimino JJ, Haskell R, Kukafka R, Matsumoto C, Chan GK, et al. Evaluation of the clinical LOINC (Logical Observation Identifiers, Names, and Codes) semantic structure as a terminology model for standardized assessment measures. J Am Med Inform Assoc. 2000 Nov-Dec [cited 2014 April 13];7(6):529-38. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129661/

  38. Jensen LJ, Bork P. Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PLoS Biol. 2010 May [cited 2014 April 13];8(5):e1000374. Avalaible in: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000374

  39. Gene Ontology Consortium (GO) [página web en internet]. What is the Gene Ontology? Berkeley: Gene Ontology. 2014 [cited 2014 April 15]. Avalaible in: http://www.geneontology.org/

  40. Courtot M, Juty N, Knupfer C, Waltemath D, Zhukova A, Drager A, et al. Controlled vocabularies and semantics in systems biology. Mol Syst Biol. 2011 [cited 2014 April 13];7:543. Avalaible in: http://msb.embopress.org/content/7/1/543.long

  41. Li C, Courtot M, Le Novere N, Laibe C. BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform. 2010 May [cited 2014 April 13];11(3):270-7. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913671/

  42. The European Bioinformatics Institute. Part of the European Molecular Biology Laboratory (EMBL-EBI) [página web en internet]. Systems Biology Ontology (SBO). Cambridge. 2014 [cited 2014 April 15]. Avalaible in: http://www.ebi.ac.uk/sbo/main/

  43. IHTSDO [página web en internet]. SNOMED CT. The Global Language of Healthcare. Copenhagen The Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT). 2014 [cited 2014 April 15]. Avalaible in: http://www.ihtsdo.org/snomed-ct/

  44. National Library of Medicine [página web en internet]. Rockville Unified Medical Language System (UMLS). 2014 [cited 2014 April 15]. Avalaible in: http://www.nlm.nih.gov/research/umls/

  45. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004 Jan 1 [cited 2014 April 15];32(Database issue):D267-70. Avalaible in: http://nar.oxfordjournals.org/content/32/suppl_1/D267.short

  46. Namli T, Dogac A. Testing conformance and interoperability of eHealth applications. Methods Inf Med. 2010 [cited 2014 April 15];49(3):281-9. Avalaible in: http://www.schattauer.de/de/magazine/uebersicht/zeitschriften-a-z/methods/contents/preprint-online/issue/special/manuscript/12951.html

  47. Ajami S, Arab-Chadegani R. Barriers to implement Electronic Health Records (EHRs). Mater Sociomed. 2013 [cited 2014 April 15];25(3):213-5. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804410/

  48. Coorevits P, Sundgren M, Klein GO, Bahr A, Claerhout B, Daniel C, et al. Electronic health records: new opportunities for clinical research. J Intern Med. 2013 Dec [cited 2014 April 15];274(6):547-60. Avalaible in: http://onlinelibrary.wiley.com/doi/10.1111/joim.12119/full

  49. Tapuria A, Kalra D, Kobayashi S. Contribution of Clinical Archetypes, and the Challenges, towards Achieving Semantic Interoperability for EHRs. Healthc Inform Res. 2013 Dec [cited 2014 April 15];19(4):286-92. Avalaible in: http://synapse.koreamed.org/search.php?where=aview&id=10.4258/hir.2013.19.4.286&code=1088HIR&vmode=FULL

  50. Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform. 2006 Sep [cited 2014 April 15];7(3):256-74. Avalaible in: http://bib.oxfordjournals.org/content/7/3/256.short

  51. Martinez M, Vazquez JM, Pereira J, Pazos A. BiOSS: A system for biomedical ontology selection. Comput Methods Programs Biomed. 2014 Apr [cited 2014 April 15];114(1):125-40. Avalaible in: http://www.sciencedirect.com/science/article/pii/S0169260714000340

  52. Rubin DL, Shah NH, Noy NF. Biomedical ontologies: a functional perspective. Brief Bioinform. 2008 Jan [cited 2014 April 15];9(1):75-90. Avalaible in: http://bib.oxfordjournals.org/content/9/1/75.short

  53. Gardner SP. Ontologies and semantic data integration. Drug Discov Today. 2005 Jul 15 [cited 2014 April 15];10(14):1001-7. Avalaible in: http://www.sciencedirect.com/science/article/pii/S135964460503504X

  54. Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, et al. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J Biomed Semantics. 2014 [cited 2014 April 15];5(1):14. Avalaible in: http://www.biomedcentral.com/content/pdf/2041-1480-5-14.pdf

  55. Ortutay C, Vihinen M. Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic Acids Res. 2009 Feb [cited 2014 April 15];37(2):622-8. Avalaible in: http://nar.oxfordjournals.org/content/37/2/622.short

  56. Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, et al. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet. 2014 Apr 3 [cited 2014 April 15];94(4):599-610. Avalaible in: http://www.sciencedirect.com/science/article/pii/S0002929714001128

  57. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009 Jul [cited 2014 April 15];37 suppl 2:170-3. Avalaible in: http://nar.oxfordjournals.org/content/early/2009/05/29/nar.gkp440.short

  58. Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, et al. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr [cited 2014 April 15];19(2):190-5. Avalaible in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277625/

  59. Surjan G. Questions on validity of International Classification of Diseases-coded diagnoses. Int J Med Inform. 1999 May [cited 2014 April 15];54(2):77-95. Avalaible in: http://www.ncbi.nlm.nih.gov/pubmed/10219948




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