Download PDF
Yearb Med Inform 2010; 19(01): 58-63
DOI: 10.1055/s-0038-1638690
Original Article
Georg Thieme Verlag KG Stuttgart

Distributed Biomedical Terminology Development: From Experiments to Open Process

C. G. Chute
1   Mayo Clinic, Rochester, MN, USA
› Author Affiliations
Further Information

Publication History

Publication Date:
07 March 2018 (online)

   Permissions and Reprints

Summary

Objective: Can social computing efforts materially alter the distributed creation and maintenance of complex biomedical terminologies and ontologies; a review of distributed authoring history and status.

Background: Social computing projects, such as Wikipedia, have dramatically altered the perception and reality of large-scale content projects and the labor required to create and maintain them. Health terminologies have become large, complex, interdependent content artifacts of increasing importance to biomedical research and the communities understanding of biology, medicine, and optimal healthcare practices. The question naturally arises as to whether social computing models and distributed authoring platforms can be applied to the voluntary, distributed authoring of high-quality terminologies and ontologies.

Methods: An historical review of distributed authoring developments.

Results: The trajectory of description logic-driven authoring tools, group process, and web-based platforms suggests that public distributed authoring is likely feasible and practical; however, no compelling example on the order of Wikipedia is yet extant. Nevertheless, several projects, including the Gene Ontology and the new revision of the International Classification of Disease (ICD-11) hold promise.

Keywords

e-Health - biomedical informatics - health informatics - education - capacity building - complex adaptive systems - information and communications technology (ICT) - applied clinical informaticians - AMIA Global Partnership Program
 

  • References:

  • 1 American_Psychiatric_Association. DSM-5: The Future of Psychiatric Diagnosis. 2010 10 Feb 2010 [cited 14 Feb 2010]; Available from: http://www.dsm5.org/Pages/Default.aspx
    PubMedGoogle Scholar
  • 2 Psychiatric Diagnosis: That way, madness lies. The Economist. 2010; 88.
    PubMedGoogle Scholar
  • 3 Baader F. The description logic handbook : theory, implementation, and applications. 2nd ed.. 2007. Cambridge, NewYork: Cambridge: University Press. xix; 601.
    Google Scholar
  • 4 Campbell KE. Distributed Development of a Logicbased Controlled Medical Terminology, in Department of Computer Science. 1997. Stanford University: Palo Alto; 289.
    Google Scholar
  • 5 Rector AL, Nowlan WA. The GALEN project. Comput Methods Programs Biomed 1994; 45 (12) 75-8.
    CrossrefPubMedGoogle Scholar
  • 6 Campbell KE, Cohn SP, Chute CG, Rennels G, Shortliffe EH. Galapagos: computer-based support for evolution of a convergent medical terminology. Proc AMIA Annu Fall Symp 1996; 269-73.
    PubMedGoogle Scholar
  • 7 Campbell KE, Cohn SP, Chute CG, Shortliffe EH, Rennels G. Scalable methodologies for distributed development of logic-based convergent medical terminology. Methods Inf Med 1998; 37 (4-5) 426-39.
    Article in Thieme ConnectPubMedGoogle Scholar
  • 8 Dolin RH, Mattison JE, Cohn S, Campbell KE, Wiesenthal AM, Hochhalter B. et al. Kaiser Permanente’s Convergent MedicalTerminology. Stud Health Technol Inform 2004; 107 (Pt 1): 346-50.
    PubMedGoogle Scholar
  • 9 Mays E, Dionne R, Weida R. K-Rep system overview. SIGART Bulletin 1991; 02 (03) 93-7.
    PubMedGoogle Scholar
  • 10 Mays E, Weida R, Dionne R, Laker M, White B, Liang C, Oles FJ. Scalable and expressive medical terminologies. Proc AMIA Annu Fall Symp 1996; 259-63.
    PubMedGoogle Scholar
  • 11 Spackman KA, Dionne R, Mays E, Weis J. Role grouping as an extension to the description logic of Ontylog, motivated by concept modeling in SNOMED. Proc AMIA Symp 2002; 712-6.
    PubMedGoogle Scholar
  • 12 Schulz S, Suntisrivaraporn B, Baader F, Boeker M. SNOMED reaching its adolescence: ontologists’ and logicians’ health check. Int J Med Inform 2009; 78 (Suppl. 01) S86-94.
    CrossrefPubMedGoogle Scholar
  • 13 IHTSDO. IHTSDO Open Sources Health Terminology Workbench. 2009 17 Dec 2009 [cited 14 Feb 2010]; Available from: http://www.ihtsdo.org/news/article/view/ihtsdo-open-sources-health-terminology-workbench/
    PubMedGoogle Scholar
  • 14 Klein B, Hoecht C, Decker B. Beyond capturing and maintaining software engineering knowledge “Wikitology” as shared semantics, in Workshop on Knowledge Engineering and Software Engineering, KI 2005. Koblenz; 2005
    PubMedGoogle Scholar
  • 15 Krötzsch M. Semantic MediaWiki. 26 Jan, 2010 [cited 16 Feb, 2010]; Available from: http://seman-tic-mediawiki.org/wiki/Main_Page
    PubMedGoogle Scholar
  • 16 CDISC. CDISC Shared Health And Clinical Research Electronic Library. 2009 2009 [cited 16 Feb 2010];Available from: http://www.cdisc.org/cdisc-share
    PubMedGoogle Scholar
  • 17 Solbrig H. Terminology Curation with the Semantic MediaWiki. in Environmental Terminology Workshop. April 2007. Vienna, Austria.
    PubMedGoogle Scholar
  • 18 Pathak J, Solbrig HR, Buntrock JD, Johnson TM, Chute CG. LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime. J Am Med Inform Assoc 2009; 16 (03) 305-15.
    CrossrefPubMedGoogle Scholar
  • 19 NCI. caBIG® Vocabulary Knowledge Center. 16 Feb 2010 [cited 16 Feb 2010]; Available from: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Main_Page
    PubMed
  • 20 NCI. Common Terminology Criteria for Adverse Events. 2009 8 February 2010 [cited 16 Feb 2010]; Available from: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/CTCAE
    PubMed
  • 21 NCI. Biomedical Grid Terminology (BiomedGT). 2008 Jan 2009 [cited 14 Feb 2010]; Available from: http://biomedgt.nci.nih.gov/wiki/index.php/Main_Page
    PubMed
  • 22 Musen MA, Eriksson H, Gennari JH, Tu SW, Puerta AR. PROTEGE-II: a suite of tools for development of intelligent systems from reusable components. Proc Annu Symp Comput Appl Med Care 1994; 1065.
    PubMedGoogle Scholar
  • 23 Noy NF, Crubezy M, Fergerson RW, Knublauch H, Tu SW, Vendetti J. et al. Protege-2000: an opensource ontology-development and knowledgeacquisition environment. AMIA Annu Symp Proc 2003; 953.
    PubMedGoogle Scholar
  • 24 Tudorache T, Noy NF, Tu S, Musen M. Supporting collaborative ontology development in Protege. Seventh International Semantic Web Conference. Karlsruhe: Springer; 2008
    Google Scholar
  • 25 Noy NF, Tudorache T, de Coronado S, Musen MA. Developing biomedical ontologies collaboratively. AMIA Annu Symp Proc 2008; 520-4.
    PubMedGoogle Scholar
  • 26 Tudorache T. Collaborative Protege. January 25, 2010 [cited 14 Feb 2010]; Available from: http://protegewiki.stanford.edu/index.php/Collaborative_Protege
    PubMedGoogle Scholar
  • 27 ICD Collaborative Authoring Tool. 2010 [cited 18 May 2010]; Available from: http://icat.stanford.edu/.
    PubMed
  • 28 Fragoso G, de Coronado S, Haber M, Hartel F, Wright L. Overview and Utilization of the NCI Thesaurus. Comp Funct Genomics 2004; 05 (08) 648-54.
    CrossrefPubMedGoogle Scholar
  • 29 de Coronado S, Wright LW, Fragoso G, Haber MW, Hahn-Dantona EA, Hartel FW. et al. The NCI Thesaurus quality assurance life cycle. J Biomed Inform 2009; 42 (03) 530-9.
    CrossrefPubMedGoogle Scholar
  • 30 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.
    PubMedGoogle Scholar
  • 31 The Gene Ontology project in 2008. Nucleic Acids Res. 2008 36. (Database issue):pD440-4.
    PubMedGoogle Scholar
  • 32 Xu T, Gu J, Zhou Y. Du L Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology. BMC Bioinformatics 2009; 10: 240.
    CrossrefPubMedGoogle Scholar
  • 33 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007; 25 (11) 1251-5.
    CrossrefPubMedGoogle Scholar
  • 34 WHO. Revision of the International Classification of Diseases (ICD). 2007 2009 [cited 14 Feb 2010]; Available from: http://www.who.int/classifications/icd/ICDRevision/en/index.html
    PubMed
  • 35 WHO. ICD 11 Channel. 2009 January 2010 [cited 16 Feb 2010]; Available from: http://www.youtube.com/user/WHOICD11
    PubMed
  • 36 (ANSI) American_National_Standards_Institute. Common Terminology Services (CTS), ANSI/HL7 CTS, V1-2005 Health Level Seven Standard: Common Terminology Services. 2005 [cited Version 1..
    PubMed
  • 37 International_Organization_for_Standardization, ISO International Standard (IS) 27951 Common Terminology Services 2009. Version 1..
    PubMedGoogle Scholar
  • 38 caBIG. LexBig and LexEVS. [cited 2010 Feb 17, 2010]; Available from: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/LexBig_and_LexEVS
    PubMed
  • 39 Pathak J, Jiang G, Dwarkanath SO, Buntrock JD, Chute CG. LexValueSets: an approach for contextdriven value sets extraction. AMIA Annu Symp Proc 2008; 556-60.
    PubMedGoogle Scholar
  • 40 National Center for Biomedical Ontology. 2010 [cited 17 Feb 2010]; Available from: http://www.bioontology.org/
    PubMed
  • 41 Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M. et al. National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. Omics 2006; 10 (02) 185-98.
    CrossrefPubMedGoogle Scholar
  • 42 Musen MA, Shah NH, Noy NF, Dai BY, Dorf M, Griffith N. et al. BioPortal: ontologies and data resources with the click of a mouse. AMIA Annu Symp Proc 2008; 1223-4.
    PubMedGoogle Scholar