Literature DB >> 19285571

A review of auditing methods applied to the content of controlled biomedical terminologies.

Xinxin Zhu1, Jung-Wei Fan, David M Baorto, Chunhua Weng, James J Cimino.   

Abstract

Although controlled biomedical terminologies have been with us for centuries, it is only in the last couple of decades that close attention has been paid to the quality of these terminologies. The result of this attention has been the development of auditing methods that apply formal methods to assessing whether terminologies are complete and accurate. We have performed an extensive literature review to identify published descriptions of these methods and have created a framework for characterizing them. The framework considers manual, systematic and heuristic methods that use knowledge (within or external to the terminology) to measure quality factors of different aspects of the terminology content (terms, semantic classification, and semantic relationships). The quality factors examined included concept orientation, consistency, non-redundancy, soundness and comprehensive coverage. We reviewed 130 studies that were retrieved based on keyword search on publications in PubMed, and present our assessment of how they fit into our framework. We also identify which terminologies have been audited with the methods and provide examples to illustrate each part of the framework.

Entities:  

Mesh:

Year:  2009        PMID: 19285571      PMCID: PMC3505841          DOI: 10.1016/j.jbi.2009.03.003

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  109 in total

1.  Modeling the UMLS using an OODB.

Authors:  H Gu; Y Perl; J Geller; M Halper; L M Liu; J J Cimino
Journal:  Proc AMIA Symp       Date:  1999

2.  Evaluation of a proposed method for representing drug terminology.

Authors:  J J Cimino; T J McNamara; T Meredith; C A Broverman; K C Eckert; M Moore; D J Tyree
Journal:  Proc AMIA Symp       Date:  1999

3.  Desiderata for a clinical terminology server.

Authors:  C G Chute; P L Elkin; D D Sherertz; M S Tuttle
Journal:  Proc AMIA Symp       Date:  1999

4.  A large-scale evaluation of terminology integration characteristics.

Authors:  F S McDonald; C G Chute; P V Ogren; D Wahner-Roedler; P L Elkin
Journal:  Proc AMIA Symp       Date:  1999

5.  Representing the UMLS as an object-oriented database: modeling issues and advantages.

Authors:  H Gu; Y Perl; J Geller; M Halper; L M Liu; J J Cimino
Journal:  J Am Med Inform Assoc       Date:  2000 Jan-Feb       Impact factor: 4.497

6.  Analysis of error concentrations in SNOMED.

Authors:  Michael Halper; Yue Wang; Hua Min; Yan Chen; George Hripcsak; Yehoshua Perl; Kent A Spackman
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

7.  Decompositional terminology translation using network analysis.

Authors:  Chintan O Patel; James J Cimino
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

8.  Piecewise synonyms for enhanced UMLS source terminology integration.

Authors:  Kuo-Chuan Huang; James Geller; Michael Halper; James J Cimino
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

9.  A comparison of two methods for retrieving ICD-9-CM data: The effect of using an ontology-based method for handling terminology changes.

Authors:  Alexander C Yu; James J Cimino
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

10.  Auditing complex concepts in overlapping subsets of SNOMED.

Authors:  Yue Wang; Duo Wei; Junchuan Xu; Gai Elhanan; Yehoshua Perl; Michael Halper; Yan Chen; Kent A Spackman; George Hripcsak
Journal:  AMIA Annu Symp Proc       Date:  2008-11-06
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  48 in total

1.  Auditing consistency and usefulness of LOINC use among three large institutions - using version spaces for grouping LOINC codes.

Authors:  M C Lin; D J Vreeman; Clement J McDonald; S M Huff
Journal:  J Biomed Inform       Date:  2012-01-28       Impact factor: 6.317

Review 2.  Literature review of SNOMED CT use.

Authors:  Dennis Lee; Nicolette de Keizer; Francis Lau; Ronald Cornet
Journal:  J Am Med Inform Assoc       Date:  2013-07-04       Impact factor: 4.497

3.  The use of semantic distance metrics to support ontology audit.

Authors:  Jian Wang; Roger Day; Shyam Visweswaran; William Hogan
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

4.  Recognition of chemical entities: combining dictionary-based and grammar-based approaches.

Authors:  Saber A Akhondi; Kristina M Hettne; Eelke van der Horst; Erik M van Mulligen; Jan A Kors
Journal:  J Cheminform       Date:  2015-01-19       Impact factor: 5.514

5.  An empirically derived taxonomy of errors in SNOMED CT.

Authors:  Jonathan M Mortensen; Mark A Musen; Natalya F Noy
Journal:  AMIA Annu Symp Proc       Date:  2014-11-14

6.  Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT.

Authors:  Jonathan M Mortensen; Evan P Minty; Michael Januszyk; Timothy E Sweeney; Alan L Rector; Natalya F Noy; Mark A Musen
Journal:  J Am Med Inform Assoc       Date:  2014-10-23       Impact factor: 4.497

7.  A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships.

Authors:  Christopher Ochs; James Geller; Yehoshua Perl; Yan Chen; Ankur Agrawal; James T Case; George Hripcsak
Journal:  J Am Med Inform Assoc       Date:  2014-10-20       Impact factor: 4.497

8.  Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies.

Authors:  Christopher Ochs; James Geller; Yehoshua Perl; Yan Chen; Junchuan Xu; Hua Min; James T Case; Zhi Wei
Journal:  J Am Med Inform Assoc       Date:  2014-10-21       Impact factor: 4.497

9.  Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.

Authors:  Ling Zheng; Hasan Yumak; Ling Chen; Christopher Ochs; James Geller; Joan Kapusnik-Uner; Yehoshua Perl
Journal:  J Biomed Inform       Date:  2017-07-16       Impact factor: 6.317

10.  An efficient, large-scale, non-lattice-detection algorithm for exhaustive structural auditing of biomedical ontologies.

Authors:  Guo-Qiang Zhang; Guangming Xing; Licong Cui
Journal:  J Biomed Inform       Date:  2018-03-13       Impact factor: 6.317

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