Literature DB >> 21907827

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

Yue Wang1, Michael Halper, Duo Wei, Huanying Gu, Yehoshua Perl, Junchuan Xu, Gai Elhanan, Yan Chen, Kent A Spackman, James T Case, George Hripcsak.   

Abstract

Auditors of a large terminology, such as SNOMED CT, face a daunting challenge. To aid them in their efforts, it is essential to devise techniques that can automatically identify concepts warranting special attention. "Complex" concepts, which by their very nature are more difficult to model, fall neatly into this category. A special kind of grouping, called a partial-area, is utilized in the characterization of complex concepts. In particular, the complex concepts that are the focus of this work are those appearing in intersections of multiple partial-areas and are thus referred to as overlapping concepts. In a companion paper, an automatic methodology for identifying and partitioning the entire collection of overlapping concepts into disjoint, singly-rooted groups, that are more manageable to work with and comprehend, has been presented. The partitioning methodology formed the foundation for the development of an abstraction network for the overlapping concepts called a disjoint partial-area taxonomy. This new disjoint partial-area taxonomy offers a collection of semantically uniform partial-areas and is exploited herein as the basis for a novel auditing methodology. The review of the overlapping concepts is done in a top-down order within semantically uniform groups. These groups are themselves reviewed in a top-down order, which proceeds from the less complex to the more complex overlapping concepts. The results of applying the methodology to SNOMED's Specimen hierarchy are presented. Hypotheses regarding error ratios for overlapping concepts and between different kinds of overlapping concepts are formulated. Two phases of auditing the Specimen hierarchy for two releases of SNOMED are reported on. With the use of the double bootstrap and Fisher's exact test (two-tailed), the auditing of concepts and especially roots of overlapping partial-areas is shown to yield a statistically significant higher proportion of errors.
Copyright © 2011 Elsevier Inc. All rights reserved.

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Year:  2011        PMID: 21907827      PMCID: PMC3313651          DOI: 10.1016/j.jbi.2011.08.016

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


  34 in total

1.  Benefits of an object-oriented database representation for controlled medical terminologies.

Authors:  H Gu; M Halper; J Geller; Y Perl
Journal:  J Am Med Inform Assoc       Date:  1999 Jul-Aug       Impact factor: 4.497

2.  Evaluation of SNOMED coverage of Veterans Health Administration terms.

Authors:  Janet F E Penz; Steven H Brown; John S Carter; Peter L Elkin; Viet N Nguyen; Shannon A Sims; Michael J Lincoln
Journal:  Stud Health Technol Inform       Date:  2004

3.  Read Code quality assurance: from simple syntax to semantic stability.

Authors:  E B Schulz; J W Barrett; C Price
Journal:  J Am Med Inform Assoc       Date:  1998 Jul-Aug       Impact factor: 4.497

4.  Reproducibility of interpreting "and" and "or" in terminology systems.

Authors:  E A Mendonça; J J Cimino; K E Campbell; K A Spackman
Journal:  Proc AMIA Symp       Date:  1998

5.  A "lexically-suggested logical closure" metric for medical terminology maturity.

Authors:  K E Campbell; M S Tuttle; K A Spackman
Journal:  Proc AMIA Symp       Date:  1998

6.  The content coverage of clinical classifications. For The Computer-Based Patient Record Institute's Work Group on Codes & Structures.

Authors:  C G Chute; S P Cohn; K E Campbell; D E Oliver; J R Campbell
Journal:  J Am Med Inform Assoc       Date:  1996 May-Jun       Impact factor: 4.497

7.  Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

Authors:  J R Campbell; P Carpenter; C Sneiderman; S Cohn; C G Chute; J Warren
Journal:  J Am Med Inform Assoc       Date:  1997 May-Jun       Impact factor: 4.497

8.  Knowledge-based approaches to the maintenance of a large controlled medical terminology.

Authors:  J J Cimino; P D Clayton; G Hripcsak; S B Johnson
Journal:  J Am Med Inform Assoc       Date:  1994 Jan-Feb       Impact factor: 4.497

9.  Auditing the Unified Medical Language System with semantic methods.

Authors:  J J Cimino
Journal:  J Am Med Inform Assoc       Date:  1998 Jan-Feb       Impact factor: 4.497

10.  Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED.

Authors:  Yue Wang; Michael Halper; Duo Wei; Yehoshua Perl; James Geller
Journal:  J Biomed Inform       Date:  2011-08-25       Impact factor: 6.317

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  29 in total

1.  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

2.  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

3.  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

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.  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

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.  A family-based framework for supporting quality assurance of biomedical ontologies in BioPortal.

Authors:  Zhe He; Christopher Ochs; Ankur Agrawal; Yehoshua Perl; Dimitris Zeginis; Konstantinos Tarabanis; Gai Elhanan; Michael Halper; Natasha Noy; James Geller
Journal:  AMIA Annu Symp Proc       Date:  2013-11-16

8.  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

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

Review 10.  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

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