The Practical Impact of Ontologies on Biomedical Informatics

Summary

Objectives

To examine recent research work in the development and evaluation of controlled biomedical terminologies – especially, the representation of structured, controlled definitional knowledge about the terms themselves; such terminologies are often referred to as “ontologies”.

Methods

A review of the published literature using PubMed, as well as full-text searches of recent Medinfo and American Medical Informatics Association (AMIA) Symposia proceedings, searching for the terms “ontology” and “ontologies” and for articles discussing specific, prominent ontological work.

Results

We summaries the ontologic aspects of twelve current terminology projects: Galen, the Unified Medical Language System (UMLS), the Medical Entities Dictionary (MED), SNOMED-CT, LOINC, the Foundational Model of Anatomy (FMA), the Gene Ontology (GO), ISO Reference Terminology Model for Nursing Diagnosis, NDF-RT, RxNorm, the NCI Thesaurus, and DOLCE+. We discuss the origins, domain, and ontologic representation of each of these and attempt to summarize the impact that each has had on terminologic work and biomedical applications. We also note the contributions of the Protégé tool to many of these efforts.

Conclusion

Terminologic research and development have advanced significantly in the past 20 years, especially since the recent orientation toward controlled biomedical ontologies. This work has had significant impact on the development of terminologies themselves, their acceptance and dissemination as standards, and their use in supporting biomedical information systems.

Keywords

Controlled Terminology - Ontology - Unified Medical Language System

• References

• 1 World Health Organization. Manual of the International Classification of Diseases, Injuries, and causes of Death. Geneva, Switzerland: 1977
• 2 Cimino JJ. Coding systems in health care. In: van Bemmel JH, McCray AT. editors. 1995 Yearbook of Medical Informatics. Stuttgart: Schattauer: 1995: 71-85.
• Reprinted in Methods Inf Med. 1996; 35 (04) 273-84.
• 3 Cimino JJ. Desiderata for controlled medical vocabularies in the Twenty-First Century. Methods Inf Med 1998; 37 4-5 394-403.
• 4 Greenes RA, McClure RC, Pattison-Gordon E, Sato L. The findings—diagnosis continuum: implications for image descriptions and clinical databases. Proc Annu Symp Comput Appl Med Care 1992; 383-7.
• 5 Musen MA. Dimensions of knowledge sharing and reuse. Comput Biomed Res 1992; Oct; 25 (05) 435-67.
• 6 Gruber TR. A translation approach to portable ontologies. Knowledge Acquisition 1993; 05 (02) 199-220.
• 7 Rector AL, Nowlan WA, Kay S. Foundations for an electronic medical record. Methods Inf Med 1991; 30 (03) 179-86.
• 8 Nowlan WA, Rector AL, Kay S, Horan B, Wilson A. A patient care workstation based on user centred design and a formal theory of medical terminology: PEN&PAD and the SMK formalism. Proceedings the Annual Symposium on Computer Applications in Medical Care 1991; 855-7.
• 9 Rector AL, Nowlan WA. The GALEN project. Comput Methods Programs Biomed 1994; Oct; 45 1-2 75-8.
• 10 Rector AL, Rogers JE, Zanstra PE, Van Der Haring E. OpenGALEN. OpenGALEN: open source medical terminology and tools. AMIA Annu Symp Proc 2003; 982.
• 11 Hardiker NR. Mediating between nursing intervention terminology systems. AMIA Annu Symp Proc 2001; 239-43.
• 12 Hardiker NR, Rector AL. Structural validation of nursing terminologies. J Am Med Inform Assoc 2001; 08 (03) 212-21.
• 13 ten Napel H, Rogers J. Assessment of the GALEN methodology on holistic classifications for professions allied to medicine. Medinfo 2001; 1369-73.
• 14 Karlsson D. A design and prototype for a decisionsupport system in the f ield of urinary tract infections—application of OpenGALEN techniques for indexing medical information. Medinfo 2001; 479-83.
• 15 Trombert-Paviot B, Rodrigues JM, Rogers JE, Baud R, van der Haring E, Rassinoux AM. et al. GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures. Int J Med Inform 2000; 58-59: 71-85.
• 16 Donnelly M. Containment relations in anatomical ontologies. AMIA Fall Symposium 2005; 206-10.
• 17 Mork P, Pottinger R, Bernstein PA. Challenges in precisely aligning models of human anatomy using generic schema matching. Medinfo 2004; 401-5.
• 18 Zhang S, Bodenreider O. Aligning representations of anatomy using lexical and structural methods. AMIA Annu Symp Proc 2003; 753-7.
• 19 http://www.nlm.nih.gov/research/umls/about_umls.html
• 20 Selden CR, Humphreys BL. Unified Medical Language System. Current Bibliographies in Medicine 1997; 08: 96.
• 21 Meystre S, Haug PJ. Evaluation of medical problem extraction from electronic clinical documents using MetaMap Transfer (MMTx). Stud Health Technol Inform 2005; 116: 823-8.
• 22 Hazlehurst B, Frost HR, Sittig DF, Stevens VJ. MediClass: A system for detecting and classifying encounter-based clinical events in any electronic medical record. J Am Med Inform Assoc 2005; Sep-Oct; 12 (05) 517-29.
• 23 Sweeney JP, Portell KS, Houck JA, Smith RD, Mentel JJ. Patient note deidentification using a find-and-replace iterative process. J Healthc Inf Manag 2005; 19 (03) 65-70.
• 24 Sadeghi S, Barzi A, Smith JW. Ontology driven construction of a knowledgebase for Bayesian decision models based on UMLS. Stud Health Technol Inform 2005; 116: 223-8.
• 25 Perez-Rey D, Maojo V, Garcia-Remesal M, Alonso-Calvo R, Billhardt H, Martin-Sanchez F. et al. ONTOFUSION: Ontology-based integration of genomic and clinical databases. Comput Biol Med. In press 2005
• 26 Bowman S. Coordinating SNOMED-CT and ICD-10. J AHIMA 2005; Jul-Aug; 76 (07) 60-1.
• 27 Slaughter LA, Soergel D, Rindflesch TC. Semantic representation of consumer questions and physician answers. Int J Med Inform. In press 2005
• 28 Cimino JJ, Clayton PD, Hripcsak G, Johnson SB. Knowledge-based approaches to the maintenance of a large controlled medical terminology. J Am Med Inform Assoc 1994; Jan-Feb; 01 (01) 35-50.
• 29 Zweigenbaum P, Bachimont B, Bouaud J, Charlet J, Boisvieux JF. Le rôle du lexique sémantique et de l’ontologie dans le traitement automatique de la langue médicale. In: Le Beux P, Burgun A. editors. Actes du Colloque CRISTAL’S. Saint-Malo; 1996
• 30 Cimino JJ. From data to knowledge through conceptoriented terminologies: experience with the Medical Entities Dictionary. J Am Med Inform Assoc 2000; May-Jun; 07 (03) 288-97.
• 31 Hwang JI, Cimino JJ, Bakken S. Integrating nursing diagnostic concepts into the medical entities dictionary using the ISO Reference Terminology Model for Nursing Diagnosis. J Am Med Inform Assoc 2003; Jul-Aug; 10 (04) 382-8.
• 32 Chiang MF, Casper DS, Cimino JJ, Starren J. Representation of ophthalmology concepts by electronic systems: adequacy of controlled medical terminologies. Ophthalmology 2005; Feb; 112 (02) 175-83.
• 33 Choi J, Jenkins ML, Cimino JJ, White TM, Bakken S. Toward semantic interoperability in home health care: formally representing OASIS items for integration into a concept-oriented terminology. J Am Med Inform Assoc 2005; Jul-Aug; 12 (04) 410-7.
• 34 Stearns MQ, Price C, Spackman KA, Wang AY. SNOMED clinical terms: overview of the development process and project status. Proc AMIA Symp 2001; 662-6.
• 35 Wang AY, Barrett JW, Bentley T, Markwell D, Price C, Spackman KA. et al. Mapping between SNOMED RT and Clinical Terms Version 3: a key component of the SNOMED CT development process. Proc AMIA Symp 2001; 741-5.
• 36 Wang AY, Sable JH, Spackman KA. The SNOMED clinical terms development process: refinement and analysis of content. Proc AMIA Symp 2002; 845-9.
• 37 Schulz S, Hahn U, Rogers J. Semantic clarification of the representation of procedures and diseases in SNOMED-CT. Stud Health Technol Inform 2005; 116: 773-8.
• 38 Burgun A, Bodenreider O, Mougin F. Classifying diseases with respect to anatomy: a study in SNOMED-CT. Proc AMIA Symp 2005; 91-5.
• 39 Fung KW, Bodenreider O. Utilizing the UMLS for semantic mapping between terminologies. Proc AMIA Symp 2005; 266-70.
• 40 Fung KW, Hole WT, Nelson SJ, Srinivasan S, Powell T, Roth L. Integrating SNOMED-CT into the UMLS: an exploration of different views of synonymy and quality of editing. J Am Med Inform Assoc 2005; 12 (04) 486-94.
• 41 Cohn SP. Seventh Annual Report to Congress on the Implementation Of the Administrative Simplification Provisions of the Health Insurance Portability and Accountability Act of 1996. September 8, 2005 www.ncvhs.hhs.gov/050908rpt.htm
• 42 Forrey AW, McDonald CJ, DeMoor G, Huff SM, Leavelle D, Leland D. et al. Logical Observation Identifiers, Names and Codes (LOINC) database: a public use set of codes and names for electronic reporting of clinical laboratory test results. Clin Chem 1996; Jan; 42 (01) 81-90.
• 43 Baorto DM, Cimino JJ, Parvin CA, Kahn MG. Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC). Int J Med Inform 1998; Jul; 51 (01) 29-37.
• 44 Cimino JJ, Meyer M, Lee NJ, Bakken S. Using patient data to retrieve health knowledge. Proc AMIA Symp 2005; 136-40.
• 45 Khan AN, Russell D, Moore C, Rosario Jr. AC, Griffith SP, Bertolli J. The map to LOINC project. Proc AMIA Symp 2003; 890.
• 46 Dolin RH, Mattison JE, Cohn S. et al. Kaiser Permanente’s Convergent Medical Terminology. Medinfo 2004; 11 (Pt 1): 346-50.
• 47 Dykes PC, Currie LM, Cimino JJ. Adequacy of evolving national standardized terminologies for interdisciplinary coded concepts in an automated clinical pathway. J Biomed Inform 2003; Aug-Oct; 36 4-5 313-25.
• 48 Parker CG, Rocha RA, Campbell JR, Tu SW, Huff SM. Detailed clinical models for sharable, executable guidelines. Medinfo 2004; 11 (Pt 1): 145-8.
• 49 Matney S, Bakken S, Huff SM. Representing nursing assessments in clinical information systems using the logical observation identifiers, names, and codes database. J Biomed Inform 2003; Aug-Oct; 36 4-5 287-93.
• 50 Rosse C, Mejino Jr JL. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003; Dec; 36 (06) 478-500.
• 51 Rosse C, Shapiro LG, Brinkley JF. The digital anatomist foundational model: principles for defining and structuring its concept domain. Proc AMIA Symp 1998; 820-4.
• 52 Rosse C, Mejino JL, Modayur BR, Jakobovits R, Hinshaw KP, Brinkley JF. Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist symbolic knowledge base. J Am Med Inform Assoc 1998; Jan-Feb; 05 (01) 17-40.
• 53 http://sig.biostr.washington.edu/projects/fm/ AboutFM.html
• 54 Shapiro LG, Chung E, Detwiler LT, Mejino Jr JLV, Agoncillo AV, Brinkley JF. et al. Processes and problems in the formative evaluation of an interface to the Foundational Model of anatomy knowledge base. J Am Med Inform Assoc 2005; 12 (01) 35-46.
• 55 WorldWideWeb Consortium. OWLWeb Ontology Language Reference. In: W3C Recommendation 10 Feb, 2004
• 56 Hartel FW, de Coronado S, Dionne R, Fragoso G, Golbeck J. Modeling a description logic vocabulary for cancer research. J Biomed Inform 2005; 38 (02) 114-29.
• 57 Dameron O, Rubin DL, Musen MA. Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. Proc AMIA Symp 2005; 181-5.
• 58 Knublauch H, Fergerson RW, Noy NF, Musen MA. The Protege OWL Plugin: An open development environment for Semantic Web applications. Semantic Web ISWC 2004, Proceedings 2004; 3298: 229-43.
• 59 Rubin DL, Dameron O, Musen MA. Use of description logic classification to reason about consequences of penetrating injuries. Proc AMIA Symp 2005; 649-53.
• 60 Warren W, Brinkley JF. Knowledge-based, interactive, custom anatomical scene creation for medical education: The Biolucida System. Proc AMIA Symp 2005; 789-93.
• 61 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; 25 (01) 25-9.
• 62 The GO Consortium. Creating the Gene Ontology resource: design and implementation. Genome Res 2001; Aug; 11 (08) 1425-33.
• 63 Coenen A, McNeil B, Bakken S, Bickford C, Warren JJ. American Nurses Association Committee on Nursing Practice Information Infrastructure. Toward comparable nursing data: American Nurses Association criteria for data sets, classification systems, and nomenclatures. Comput Nurs 2001; Nov-Dec; 19 (06) 240-8.
• 64 Warren JJ, Mead CN, Button P, Henry SB, Androwich I. Development of the Loose Canon Model of nursing interventions represented using the Unified Modeling Language (UML). Proc AMIA Symp 1999; 1189.
• 65 Moss J, Coenen A, Mills ME. Evaluation of the draft international standard for a reference terminology model for nursing actions. J Biomed Inform 2003; Aug-Oct; 36 4-5 271-8.
• 66 International Standards Organization. Integration of a Reference Terminology Model for Nursing - FDIS. Geneva, Switzerland: International Standards Organization; 2003
• 67 Harris M, Kim H, Rhudy L, Savova G, Chute C. Testing the generalizability of the ISO model for nursing diagnoses. AMIA Annu Symp Proc 2003; 274-8.
• 68 Bakken S, Hyun S, Friedman C, Johnson SB. ISO reference terminology models for nursing: applicability for natural language processing of nursing narratives. Int J Med Inform 2005; Aug; 74 7-8 615-22.
• 69 Junttila K, Salantera S, Hupli M. Developing terminology for documenting perioperative nursing interventions. Int J Med Inform 2005; Jul; 74 (06) 461-71.
• 70 Brown SH, Lincoln MJ, Groen P, Kolodner RM. VistA: The U.S. Department of Veterans Affairs national-scale Hospital Information System. Int J Med Inform 2003; 69 (2/3): 135-56.
• 71 Carter JS, Brown SH, Erlbaum MS, Gregg W, Elkin PL, Speroff T. et al. Initializing the VA Medication Reference Terminology using UMLS Metathesaurus co-Occurrences. Proc AMIA Symp 2002; 116-20.
• 72 Rosenbloom S, Awad J, Speroff T, Elkin P, Rothman R, Spickard AI. et al. Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications. Proc AMIA 2003; 569-73.
• 73 United States Pharmacopeia Medicare Model Guidelines Expert Committee. United States Pharmacopeia Medicare Model Guidelines. October 8, 2004
• 74 Brown SH, Elkin PL, Rosenbloom ST, Husser C, Bauer BA, Lincoln MJ. et al. VA National Drug File Reference Terminology: a cross-institutional content coverage study. Medinfo 2004; 11 (Pt 1): 477-81.
• 75 Lincoln MJ, Brown SH, Nguyen V, Cromwell T, Carter J, Erlbaum M. et al. U.S. Department of Veterans Affairs Enterprise Reference Terminology strategic overview. Medinfo 11 (Pt 1): 391-5. 2004;
• 76 http://www.nlm.nih.gov/research/umls/rxnorm/
• 77 Cimino JJ, McNamara TJ, Meredith T, Broverman CA, Eckert KC, Moore M. et al. Evaluation of a proposed method for representing drug terminology. J Am Med Inform Assoc 1999; 06 (suppl.): 47-51.
• 78 http://nciterms.nci.nih.gov/NCIBrowser/ Dictionary.do
• 79 de Coronado S, Haber MW, Sioutos N, Tuttle MS, Wright LW. NCI Thesaurus: using science-based terminology to integrate cancer research results. Medinfo 2004; 11 (Pt 1): 33-7.
• 80 Hubbard SM, Martin NB, Blankenbaker LW, Esterhay Jr RJ, Masys DR, Tingley DE. et al. The Physician Data Query (PDQ) cancer information system. J Cancer Educ 1986; 01 (02) 79-87.
• 81 Apelon. http://www.apelon.com/products/products.htm
• 82 Smith MK, Welty C, McGuinness DL. OWL Web Ontology Language Guide. http://www.w3.org/TR/owl-guide/2003
• 83 Souripriya Das. et al. Building Semantically Rich Life Science Applications using OWL Ontologies in Oracle. September, 2004
• 84 Ceusters W, Smith B, Goldberg L. A terminological and ontological analysis of the NCI Thesaurus. Methods Inf Med 2005; 44: 498-507.
• 85 Masolo C, Borgo S, Gangemi A, Guarino N, Oltramari A, Schneider L. The WonderWeb Library of foundational ontologies. WonderWeb Deliverable 18 . http://wonderweb.semanticweb.org 2003
• 86 Pisanelli DM, Gangemi A, Battaglia M, Catenacci C. Coping with medical polysemy in the semantic web: the role of ontologies. Medinfo 2004; 11 (Pt 1): 416-9.
• 87 Tu SW, Eriksson H, Gennari JH, Shahar Y, Musen MA. Ontology-based configuration of problemsolving methods and generation of knowledgeacquisition tools: application of PROTEGE-II to protocol-based decision support. Artif Intell Med 1995; 07 (03) 257-89.
• 88 Gennari J, Musen MA, Fergerson RW, Grosso WE, Crubézy M, Eriksson H. et al. The evolution of Protégé: an environment for knowledge-based systems development. Int J Hum Comput Stud 2003; 58 (01) 89-123.
• 89 Volker RMHaarslev. Description of the RACER system and its applications. International Workshop on Description Logics (DL-2001). 2001 August 13; Stanford, USA: 2001
• 90 Noy NF, Crubezy M, Fergerson RW. et al. Protégé2000: An open-source ontology-development and knowledge-acquisition environment. Proc AMIA Symp 2003; 953.
• 91 Shankar RD, Tu SW, Musen MA. A knowledgeacquisition wizard to encode guidelines. Proc AMIA Symp 2003; 1007.
• 92 Park JY, Musen MA. VM-in-Protege: a study of software reuse. Medinfo 1998; 9 Pt 1: 644-8.
• 93 Bang M, Eriksson H. Generation of development environments for the Arden Syntax. Proc AMIA Symp 1997; 313-7.
• 94 Yeh I, Karp PD, Noy NF, Altman RB. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics 2003; 19 (02) 241-8.
• 95 Lambrix P, Habbouche M, Perez M. Evaluation of ontology development tools for bioinformatics. Bioinformatics 2003; 19 (12) 1564-71.
• 96 Detwiler LT, Mejino Jr JV, Rosse C, Brinkley JF. Structural Informatics Group. Efficient web-based navigation of the Foundational Model of Anatomy. AMIA Annu Symp Proc 2003; 829.
• 97 Jiang G, Ogasawara K, Endoh A, Sakurai T. Contextbased ontology building support in clinical domains using formal concept analysis. Int J Med Inform 2003; 71 (01) 71-81.
• 98 Zhou X, Wu Z, Yin A, Wu L, Fan W, Zhang R. Ontology development for unified traditional Chinese medical language system. Artif Intell Med 2004; 32 (01) 15-27.
• 99 Fan L, Smith A, Boenning D, Castro G, Champagne S, Loeb JM. et al. Building a hospital incident reporting ontology (HIRO) in the Web Ontology Language (OWL) using the JCAHO Patient Safety Event Taxonomy (PSET). Proc AMIA Symp 2005; 952.
• 100 Vishwanath K, Viswanath V, Drake W, Lee Y. OntoDiagram: automatic diagram generation for congenital heart defects in pediatric cardiology. Proc AMIA Symp 2005; 754-8.
• 101 Zhang S, Bodenreider O. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. Proc AMIA Symp 2005; 864-8.
• 102 Supekar K, Chute CG, Solbrig H. Representing lexical components of medical terminologies in OWL. Proc AMIA Symp 2005; 719-23.
• 103 U.S. General Accounting Office. Automated Medical Records Leadership Needed to Expedite Standards Development. GAO/IMTEX-93-17. Washingon, D.C: April 30, 1993
• 104 Jenders RA, Sujansky W, Broverman CA, Chadwick M. Towards improved knowledge sharing: assessment of the HL7 Reference Information Model to support medical logic module queries. Proc AMIA Annu Fall Symp 1997; 308-12.