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Cited by 368Biomedical Text Mining and OntologiesSemantic Web and OntologiesElectronic Health Records Systems

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

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Bodenreider, O.·2008·Yearbook of Medical Informatics
DOI 10.1055/s-0038-1638585PMC PMC2592252
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Abstract

Summary: Objectives To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support. MethodsBiomedical ontologies selected for their practical impact are examined from a functional perspective. Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles. Results The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm, the National Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS). The roles played by biomedical ontologies are classified into three major categories: knowledge management (indexing and retrieval of data and information, access to information, mapping among ontologies); data integration, exchange and semantic interoperability; and decision support and reasoning (data selection and aggregation, decision support, natural language processing applications, knowledge discovery). Conclusions Ontologies play an important role in biomedical research through a variety of applications. While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge. Barriers to the use of ontologies in biomedical applications are discussed. Geissbuhler A, Kulikowski C, editors. IMIA Year book of Medical Informatics 2008.

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  • Knowledge graphs over many fields have been constructed, e.g., SNOMED-CT in medical field, HowNet in Chinese conception.

    “As knowledge refined into a structured form, KGs over many fields have been constructed, e.g., SNOMED-CT (Bodenreider 2008) in medical field, HowNet (Dong, Dong, and Hao 2006) in Chinese conception.”

    From K-BERT: Enabling Language Representation with Knowledge Graph (2020) · cites this paper as Bodenreider 2008

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References 198 · Cited by 368

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Research works printed but not linked: 53

  1. Gersenovic M. The ICD family of classifications. Methods Inf Med 1995;34(1-2):172-5.
  2. McCray AT. Conceptualizing the world: lessons from history. J Biomed Inform 2006;39(3):267-73.
  3. Chute CG. Clinical classification and terminology: some history and current observations. J Am Med Inform Assoc 2000;7(3):298-303.
  4. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a reference terminology for ontology research and development in the biomedical domain. In: Bodenreider O, editor. Proceedings of the Se- cond International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2006); 2006. p. 57-65.
  5. Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform 2006;7(3):256-74.
  6. Coonan KM. Medical informatics standards applicable to emergency department information systems: making sense of the jumble. Acad Emerg Med 2004;11(11):1198-205.
  7. Yu AC. Methods in biomedical ontology. J Biomed Inform 2006;39(3):252-66.
  8. Bodenreider O, Burgun A. Biomedical ontologies. In: Chen H, Fuller S, Hersh WR, Friedman C, editors. Medical informatics: Advances in knowl- edge management and data mining in biomedicine. New York: Springer-Verlag; 2005. p. 211-36.
  9. Huff SM. Ontologies, vocabularies, and data mod- els. In: Greenes RA, editor. Clinical desision sup- port: The road ahead. Amsterdam: Academic Press; 2007. p. 307-24.
  10. Lussier YA, Bodenreider O. Clinical ontologies for discovery applications. In: Baker CJO, Cheung K- H, editors. Semantic Web: Revolutionizing knowl- edge discovery in the life sciences. New York: Springer; 2007. p. 101-19.
  11. Stevens R, Wroe C, Lord P, Goble C. Ontologies in bioinformatics. In: Staab S, Studer R, editors. Handbook on ontologies. Berlin ; New York: Springer; 2004. p. 635-57.
  12. Rubin DL, Shah NH, Noy NF. Biomedical ontolo- gies: a functional perspective. Brief Bioinform 2008;9(1):75-90.
  13. Baorto DM, Cimino JJ, Parvin CA, Kahn MG. Combining laboratory data sets from multiple in- stitutions using the logical observation identifier names and codes (LOINC). Int J Med Inform 1998;51(1):29-37.
  14. Burgun A. Desiderata for domain reference ontolo- gies in biomedicine. J Biomed Inform 2006;39(3):307-13.
  15. Rosse C, Mejino JL, Jr. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003;36(6):478-500.
  16. Donnelly K. SNOMED-CT: The advanced termi- nology and coding system for eHealth. Stud Health Technol Inform 2006;121:279-90.
  17. Huff SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood WD, Jr., et al. Development of the Logical Observation Identifiers Names and Codes (LOINC) vocabulary. J Am Med Inform Assoc 1998;5(3):276-92.
  18. McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R, et al. LOINC, a universal standard for identifying laboratory observations: a 5-year up- date. Clin Chem 2003;49(4):624-33.
  19. Lomax J. Get ready to GO! A biologist's guide to the Gene Ontology. Brief Bioinform 2005;6(3):298-304.
  20. Liu S, Wei M, Moore R, Ganesan VAGV, Nelson SANS. RxNorm: prescription for electronic drug information exchange. IT Professional 2005;7(5):17-23.
  21. Sioutos N, de Coronado S, Haber MW, Hartel FW, Shaiu WL, Wright LW. NCI Thesaurus: a semantic model integrating cancer-related clinical and mo- lecular information. J Biomed Inform 2007;40(1):30-43.
  22. Jakob R, Ustun B, Madden R, Sykes C. The WHO Family of International Classifications. Bundes- gesundheitsblatt Gesundheitsforschung Gesund- heitsschutz 2007;50(7):924-31.
  23. Lindberg DA, Humphreys BL, McCray AT. The Unified Medical Language System. Methods Inf Med 1993;32(4):281-91.
  24. Kolarik C, Hofmann-Apitius M, Zimmermann M, Fluck J. Identification of new drug classification terms in textual resources. Bioinformatics 2007;23(13):i264-72.
  25. Blake JA, Bult CJ. Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 2006;39(3):314-20.
  26. Richesson RL, Andrews JE, Krischer JP. Use of SNOMED CT to represent clinical research data: a semantic characterization of data items on case re- port forms in vasculitis research. J Am Med Inform Assoc 2006;13(5):536-46.
  27. Friedman C, Shagina L, Lussier Y, Hripcsak G. Automated encoding of clinical documents based on natural language processing. J Am Med Inform Assoc 2004;11(5):392-402.
  28. Pakhomov SV, Buntrock JD, Chute CG. Automat- ing the assignment of diagnosis codes to patient encounters using example-based and machine learn- ing techniques. J Am Med Inform Assoc 2006;13(5):516-25.
  29. Pestian JP, Brew C, Matykiewicz P, Hovermale D, Johnson N, Cohen KB, et al. A shared task involv- ing multi-label classification of clinical free text. In: Biological, translational, and clinical language processing; 2007 2007-06; Prague, Czech Repub- lic: Association for Computational Linguistics; 2007. p. 97-104.
  30. Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R, et al. GOAnnotator: linking protein GO annotations to evidence text. J Biomed Discov Collab 2006;1:19.
  31. Crangle CE, Zbyslaw A. Identifying gene ontology concepts in natural-language text. Conf Proc IEEE Eng Med Biol Soc 2004;4:2821-3.
  32. Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. Automatic extraction of gene ontology annota- tion and its correlation with clusters in protein networks. BMC Bioinformatics 2007;8:243.
  33. Tuttle MS, Olson NE, Keck KD, Cole WG, Erlbaum MS, Sherertz DD, et al. Metaphrase: an aid to the clinical conceptualization and formalization of pa- tient problems in healthcare enterprises. Methods Inf Med 1998;37(4-5):373-83.
  34. Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through web services: calling Whatizit. Bioinformatics 2008;24:296-8.
  35. Srinivasan P. Retrieval feedback in MEDLINE. J Am Med Inform Assoc 1996;3(2):157-67.
  36. Brandt C, Nadkarni P. Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods. Comput Methods Programs Biomed 2001;64(1):37-43.
  37. Bratsas C, Koutkias V, Kaimakamis E, Bamidis P, Maglaveras N. Ontology-based Vector Space Model and Fuzzy Query Expansion to Retrieve Knowl- edge on Medical Computational Problem Solu- tions. Conf Proc IEEE Eng Med Biol Soc 2007;1:3794-7.
  38. Lowe HJ, Antipov I, Hersh W, Smith CA, Mailhot M. Automated semantic indexing of imaging re- ports to support retrieval of medical images in the multimedia electronic medical record. Methods Inf Med 1999;38(4-5):303-7.
  39. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics 2006;22 (14):e547-56.
  40. Ide NC, Loane RF, Demner-Fushman D. Essie: a con- cept-based search engine for structured biomedical text. J Am Med Inform Assoc 2007;14(3):253-63.
  41. Muller HM, Kenny EE, Sternberg PW. Textpresso: an ontology-based information retrieval and extrac- tion system for biological literature. PLoS Biol 2004;2(11):e309.
  42. Gaudinat A, Ruch P, Joubert M, Uziel P, Strauss A, Thonnet M, et al. Health search engine with e- document analysis for reliable search results. Int J Med Inform 2006;75(1):73-85.
  43. Can AB, Baykal N. MedicoPort: a medical search engine for all. Comput Methods Programs Biomed 2007;86(1):73-86.
  44. Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC. Knowledge-based meth- ods to help clinicians find answers in MEDLINE. J Am Med Inform Assoc 2007;14(6):772-80.
  45. Haynes RB, McKibbon KA, Wilczynski NL, Walter SD, Werre SR. Optimal search strategies for retriev- ing scientifically strong studies of treatment from Medline: analytical survey. BMJ 2005;330 (7501):1179.
  46. Whetzel PL, Parkinson H, Stoeckert CJ, Jr. Using ontologies to annotate microarray experiments. Methods Enzymol 2006;411:325-39.
  47. Boulos MN. A first look at HealthCyberMap medi- cal semantic subject search engine. Technol Health Care 2004;12(1):33-41.
  48. Lee M, Wang W, Yu H. Exploring supervised and unsupervised methods to detect topics in biomedi- cal text. BMC Bioinformatics 2006;7:140.
  49. Yamamoto Y, Takagi T. Biomedical knowledge navigation by literature clustering. J Biomed In- form 2007;40(2):114-30.
  50. Noyes K, Liu H, Holloway R, Dick AW. Accu- racy of Medicare claims data in identifying Par- kinsonism cases: comparison with the Medicare current benef iciary survey. Mov Disord 2007;22(4):509-14. 138. Schneeweiss S, Robicsek A, Scranton R, Zuckerman D, Solomon DH. Veteran's affairs hos- pital discharge databases coded serious bacterial infections accurately. J Clin Epidemiol 2007;60(4):397-409. 139. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998;95(25):14863-8. 140. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA. Global functional profiling of gene expression. Genomics 2003;81(2):98-104. 141. Gene Ontology Tools. http://geneontology.org/ GO.tools.shtml 142.
  51. Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S. Recent additions and im- provements to the Onto-Tools. Nucleic Acids Res 2005;33(Web Server issue):W762-5. 143. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003;4(4):R28. 144. Zhang B, Schmoyer D, Kirov S, Snoddy J. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 2004;5:16. 145. Djebbari A, Karamycheva S, Howe E, Quackenbush J. MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinformatics 2005;21(15):3324-6. 146. Bresell A, Servenius B, Persson B. Ontology annotation treebrowser : an interactive tool where the complementarity of medical subject head- ings and gene ontology improves the interpreta- tion of gene lists. Appl Bioinformatics 2006;5(4):225-36. 147. Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Inter- preting microarray results with gene ontology and MeSH. Methods Mol Biol 2007;377:223-42. 148. Brameier M, Wiuf C. Co-clustering and visual- ization of gene expression data and gene ontol- ogy terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform 2007;40(2):160-73. 149. Huang D, Wei P, Pan W. Combining gene anno- tations and gene expression data in model-based clustering: weighted method. OMICS 2006;10(1):28-39. 150. Liu J, Wang W, Yang J. Gene Ontology friendly biclustering of expression profiles. Proc IEEE Comput Syst Bioinform Conf 2004:436-47. 151. Lord PW, Stevens RD, Brass A, Goble CA. Se- mantic similarity measures as tools for exploring the gene ontology. Pac Symp Biocomput 2003:601-12. 152. Wolting C, McGlade CJ, Tritchler D. Cluster analysis of protein array results via similarity of Gene Ontology annotation. BMC Bioinformatics 2006;7:338. 153. Achour SL, Dojat M, Rieux C, Bierling P, Lepage E. A UMLS-based knowledge acquisition tool for rule-based clinical decision support system development. J Am Med Inform Assoc 2001;8(4):351-60. 154. Kashyap V, Morales A, Hongsermeier T. On imple- menting clinical decision support: achieving scalability and maintainability by combining busi- ness rules and ontologies. AMIA Annu Symp Proc 2006:414-8. 155. Greenes RA. Clinical decision support : the road ahead. Amsterdam ; Boston: Elsevier Academic Press; 2007. 156. Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P, Musen MA. Using ontologies linked with geometric models to reason about penetrating injuries. Artif Intell Med 2006;37(3):167-76. 157. Marquet G, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL- DL and NCI Thesaurus. AMIA Annu Symp Proc 2007:508-12. 158. Wolstencroft KJ, Stevens R, Tabernero L, Brass A. PhosphaBase: an ontology-driven database re- source for protein phosphatases. Proteins 2005;58(2):290-4. 159. Uzuner O, Goldstein I, Luo Y, Kohane I. Identi- fying patient smoking status from medical dis- charge records. J Am Med Inform Assoc 2008;15(1):14-24. 160. Meystre S, Haug PJ. Natural language processing to extract medical problems from electronic clini- cal documents: performance evaluation. J Biomed Inform 2006;39(6):589-99. 161. Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC. Identifying respi- ratory findings in emergency department reports for biosurveillance using MetaMap. Medinfo 2004;11(Pt 1):487-91. 162. BioCaster. http://biocaster.nii.ac.jp/ 163. EpiSpider. http://www.epispider.org/ 164.
  52. Rindflesch TC, Fiszman M, Libbus B. Semantic interpretation for the biomedical literature. In: Chen H, Fuller S, Hersh WR, Friedman C, edi- tors. Medical informatics: Advances in knowl- edge management and data mining in biomedi- cine: Springer-Verlag; 2005. p. 399-422. 165. Friedman C, Alderson PO, Austin JH, Cimino JJ, Johnson SB. A general natural-language text processor for clinical radiology. J Am Med In- form Assoc 1994;1(2):161-74. 166. Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C. PhenoGO: assigning phenotypic con- text to gene ontology annotations with natural language processing. Pac Symp Biocomput 2006:64-75. 167. Tessi. http://www.landcglobal.com/pages/ tessi_indexing.php 168. Jacquemart P, Zweigenbaum P. Towards a medi- cal question-answering system: a feasibility study. Stud Health Technol Inform 2003;95:463-8. 169. Terol RM, Martinez-Barco P, Palomar M. A knowledge based method for the medical ques- tion answering problem. Comput Biol Med 2007;37(10):1511-21. 170. Wedgwood J. MQAF: a medical question-answer- ing framework. AMIA Annu Symp Proc 2005:1150. 171. EAGLi. http://eagl.unige.ch/EAGLi/ 172.
  53. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. The OBO Foundry: coordi- nated evolution of ontologies to support bio- medical data integration. Nat Biotechnol 2007;25(11):1251-5. 203. Rogers JE. Quality assurance of medical ontolo- gies. Methods Inf Med 2006;45(3):267-74. 204. Smith B. The evaluation of ontologies: editorial review vs. democratic ranking. Proceedings of the First Interdisciplinary Ontology Meeting 2008:29-36. Correspondence to: Dr. Olivier Bodenreider National Library of Medicine 8600 Rockville Pike -MS 3841 (Bldg 38A, Rm B1N28U) Bethesda, MD 20894 -USA Tel: +1 301 435 3246 Fax: +1 301 480 3035

Authors
Bodenreider, O.
Affiliations
National Institutes of Health (US)
Corresponding author
Bodenreider, O.
ORCID
Bodenreider, O.
Venue
Yearbook of Medical Informatics
Publisher
Georg Thieme Verlag KG
Published
2008-08
Volume
17
Issue
01
Pages
67-79
ISSN
  • 0943-4747 (ISSN-L)
  • 2364-0502
DOI
10.1055/s-0038-1638585
PMC
PMC2592252
OpenAlex
W2156997379
Cited by
368
References
198
Citations by year
2026: 5 · 2025: 7 · 2024: 11 · 2023: 14 · 2022: 16 · 2021: 22 · 2020: 15 · 2019: 16 · 2018: 34 · 2017: 26 · 2016: 38 · 2015: 24 · 2014: 27 · 2013: 32 · 2012: 26
FWCI
7.55
Type
journal article
Language
en
Open access
Licence
public-domain
Locations
  • Yearbook of Medical Informatics (publishedVersion, public-domain)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health (Z99 LM999999)
  • U.S. National Library of Medicine
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
  • Health Sciences › Health Professions › Health Information Management › Electronic Health Records Systems
Keywords
biomedical ontologies, knowledge management, data integration, clinical decision support, semantic interoperability, ontology mapping, SNOMED CT, LOINC, Foundational Model of Anatomy, Gene Ontology, RxNorm, NCI Thesaurus, ICD, Medical Subject Headings, UMLS, terminology standardization, natural language processing, knowledge discovery
MeSH terms
Decision Support Techniques, Natural Language Processing, Terminology as Topic, Semantics, Bibliometrics, Vocabulary, Controlled, Information Management, PubMed

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