Literature DB >> 25336594

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

Christopher Ochs1, James Geller1, Yehoshua Perl1, Yan Chen2, Junchuan Xu3, Hua Min4, James T Case5, Zhi Wei1.   

Abstract

OBJECTIVE: Standards terminologies may be large and complex, making their quality assurance challenging. Some terminology quality assurance (TQA) methodologies are based on abstraction networks (AbNs), compact terminology summaries. We have tested AbNs and the performance of related TQA methodologies on small terminology hierarchies. However, some standards terminologies, for example, SNOMED, are composed of very large hierarchies. Scaling AbN TQA techniques to such hierarchies poses a significant challenge. We present a scalable subject-based approach for AbN TQA.
METHODS: An innovative technique is presented for scaling TQA by creating a new kind of subject-based AbN called a subtaxonomy for large hierarchies. New hypotheses about concentrations of erroneous concepts within the AbN are introduced to guide scalable TQA.
RESULTS: We test the TQA methodology for a subject-based subtaxonomy for the Bleeding subhierarchy in SNOMED's large Clinical finding hierarchy. To test the error concentration hypotheses, three domain experts reviewed a sample of 300 concepts. A consensus-based evaluation identified 87 erroneous concepts. The subtaxonomy-based TQA methodology was shown to uncover statistically significantly more erroneous concepts when compared to a control sample. DISCUSSION: The scalability of TQA methodologies is a challenge for large standards systems like SNOMED. We demonstrated innovative subject-based TQA techniques by identifying groups of concepts with a higher likelihood of having errors within the subtaxonomy. Scalability is achieved by reviewing a large hierarchy by subject.
CONCLUSIONS: An innovative methodology for scaling the derivation of AbNs and a TQA methodology was shown to perform successfully for the largest hierarchy of SNOMED.
© The Author 2014. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Entities:  

Keywords:  SNOMED CT; abstraction network; scalable quality assurance; standards quality assurance; subject-based terminology quality assurance; terminology quality assurance

Mesh:

Year:  2014        PMID: 25336594      PMCID: PMC6283060          DOI: 10.1136/amiajnl-2014-003151

Source DB:  PubMed          Journal:  J Am Med Inform Assoc        ISSN: 1067-5027            Impact factor:   4.497


  35 in total

1.  Health information technology: initial set of standards, implementation specifications, and certification criteria for electronic health record technology. Final rule.

Authors: 
Journal:  Fed Regist       Date:  2010-07-28

2.  The semantics of procedures and diseases in SNOMED CT.

Authors:  S Schulz; S Hanser; U Hahn; J Rogers
Journal:  Methods Inf Med       Date:  2006       Impact factor: 2.176

3.  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

Review 4.  A review of auditing methods applied to the content of controlled biomedical terminologies.

Authors:  Xinxin Zhu; Jung-Wei Fan; David M Baorto; Chunhua Weng; James J Cimino
Journal:  J Biomed Inform       Date:  2009-03-12       Impact factor: 6.317

5.  Auditing the semantic completeness of SNOMED CT using formal concept analysis.

Authors:  Guoqian Jiang; Christopher G Chute
Journal:  J Am Med Inform Assoc       Date:  2008-10-24       Impact factor: 4.497

6.  New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content.

Authors:  James Geller; Christopher Ochs; Yehoshua Perl; Junchuan Xu
Journal:  AMIA Annu Symp Proc       Date:  2012-11-03

7.  Scalability of abstraction-network-based quality assurance to large SNOMED hierarchies.

Authors:  Christopher Ochs; Yehoshua Perl; James Geller; Michael Halper; Huanying Gu; Yan Chen; Gai Elhanan
Journal:  AMIA Annu Symp Proc       Date:  2013-11-16

8.  Identifying inconsistencies in SNOMED CT problem lists using structural indicators.

Authors:  Ankur Agrawal; Yehoshua Perl; Yan Chen; Gai Elhanan; Mei Liu
Journal:  AMIA Annu Symp Proc       Date:  2013-11-16

Review 9.  Auditing complex concepts of SNOMED using a refined hierarchical abstraction network.

Authors:  Yue Wang; Michael Halper; Duo Wei; Huanying Gu; Yehoshua Perl; Junchuan Xu; Gai Elhanan; Yan Chen; Kent A Spackman; James T Case; George Hripcsak
Journal:  J Biomed Inform       Date:  2011-09-01       Impact factor: 6.317

10.  Overview and utilization of the NCI thesaurus.

Authors:  Gilberto Fragoso; Sherri de Coronado; Margaret Haber; Frank Hartel; Larry Wright
Journal:  Comp Funct Genomics       Date:  2004
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  27 in total

1.  Identifying Similar Non-Lattice Subgraphs in Gene Ontology based on Structural Isomorphism and Semantic Similarity of Concept Labels.

Authors:  Rashmie Abeysinghe; Xufeng Qu; Licong Cui
Journal:  AMIA Annu Symp Proc       Date:  2018-12-05

2.  Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing.

Authors:  Ling Zheng; Hao Liu; Yehoshua Perl; James Geller; Christopher Ochs; James T Case
Journal:  AMIA Annu Symp Proc       Date:  2018-12-05

3.  A lexical-based approach for exhaustive detection of missing hierarchical IS-A relations in SNOMED CT.

Authors:  Fengbo Zheng; Jay Shi; Licong Cui
Journal:  AMIA Annu Symp Proc       Date:  2021-01-25

4.  Tracking the Remodeling of SNOMED CT's Bacterial Infectious Diseases.

Authors:  Christopher Ochs; James T Case; Yehoshua Perl
Journal:  AMIA Annu Symp Proc       Date:  2017-02-10

5.  Is the Application of SNOMED CT Concept Model sufficiently Quality Assured?

Authors:  J M Rodrigues; S Schulz; B Mizen; A Rector; S Serir
Journal:  AMIA Annu Symp Proc       Date:  2018-04-16

6.  Quality Assurance of NCI Thesaurus by Mining Structural-Lexical Patterns.

Authors:  Rashmie Abeysinghe; Michael A Brooks; Jeffery Talbert; Cui Licong
Journal:  AMIA Annu Symp Proc       Date:  2018-04-16

7.  Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.

Authors:  Ling Zheng; Yan Chen; Gai Elhanan; Yehoshua Perl; James Geller; Christopher Ochs
Journal:  J Biomed Inform       Date:  2018-05-28       Impact factor: 6.317

8.  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

Review 9.  Introducing the Big Knowledge to Use (BK2U) challenge.

Authors:  Yehoshua Perl; James Geller; Michael Halper; Christopher Ochs; Ling Zheng; Joan Kapusnik-Uner
Journal:  Ann N Y Acad Sci       Date:  2016-10-17       Impact factor: 5.691

10.  A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

Authors:  Christopher Ochs; James Geller; Yehoshua Perl; Mark A Musen
Journal:  J Biomed Inform       Date:  2016-06-23       Impact factor: 6.317

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