Literature DB >> 20841848

Using the abstraction network in complement to description logics for quality assurance in biomedical terminologies - a case study in SNOMED CT.

Duo Wei1, Olivier Bodenreider.   

Abstract

OBJECTIVES: To investigate errors identified in SNOMED CT by human reviewers with help from the Abstraction Network methodology and examine why they had escaped detection by the Description Logic (DL) classifier. Case study; Two examples of errors are presented in detail (one missing IS-A relation and one duplicate concept). After correction, SNOMED CT is reclassified to ensure that no new inconsistency was introduced.
CONCLUSIONS: DL-based auditing techniques built in terminology development environments ensure the logical consistency of the terminology. However, complementary approaches are needed for identifying and addressing other types of errors.

Entities:  

Mesh:

Year:  2010        PMID: 20841848      PMCID: PMC4303368     

Source DB:  PubMed          Journal:  Stud Health Technol Inform        ISSN: 0926-9630


  10 in total

1.  Auditing SNOMED relationships using a converse abstraction network.

Authors:  Duo Wei; Michael Halper; Gai Elhanan; Yan Chen; Yehoshua Perl; James Geller; Kent A Spackman
Journal:  AMIA Annu Symp Proc       Date:  2009-11-14

2.  Mistakes in medical ontologies: where do they come from and how can they be detected?

Authors:  Werner Ceusters; Barry Smith; Anand Kumar; Christoffel Dhaen
Journal:  Stud Health Technol Inform       Date:  2004

3.  Structural methodologies for auditing SNOMED.

Authors:  Yue Wang; Michael Halper; Hua Min; Yehoshua Perl; Yan Chen; Kent A Spackman
Journal:  J Biomed Inform       Date:  2006-12-24       Impact factor: 6.317

4.  Auditing description-logic-based medical terminological systems by detecting equivalent concept definitions.

Authors:  Ronald Cornet; Ameen Abu-Hanna
Journal:  Int J Med Inform       Date:  2007-08-10       Impact factor: 4.046

5.  Special issue on auditing of terminologies.

Authors:  J Geller; Y Perl; M Halper; R Cornet
Journal:  J Biomed Inform       Date:  2009-06       Impact factor: 6.317

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.  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

8.  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

9.  Why do it the hard way? The case for an expressive description logic for SNOMED.

Authors:  Alan L Rector; Sebastian Brandt
Journal:  J Am Med Inform Assoc       Date:  2008-08-28       Impact factor: 4.497

10.  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
  10 in total
  15 in total

1.  Dissimilarities in the Logical Modeling of Apparently Similar Concepts in SNOMED CT.

Authors:  Ankur Agrawal; Gai Elhanan; Michael Halper
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

2.  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

3.  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

4.  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

5.  Quality assurance in LOINC using Description Logic.

Authors:  Tomasz Adamusiak; Olivier Bodenreider
Journal:  AMIA Annu Symp Proc       Date:  2012-11-03

6.  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

Review 7.  Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

Authors:  Muhammad Amith; Zhe He; Jiang Bian; Juan Antonio Lossio-Ventura; Cui Tao
Journal:  J Biomed Inform       Date:  2018-02-17       Impact factor: 6.317

Review 8.  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

9.  Using SPARQL to Test for Lattices: application to quality assurance in biomedical ontologies.

Authors:  Guo-Qiang Zhang; Olivier Bodenreider
Journal:  Semant Web ISWC       Date:  2010

10.  An analysis of FMA using structural self-bisimilarity.

Authors:  Lingyun Luo; José L V Mejino; Guo-Qiang Zhang
Journal:  J Biomed Inform       Date:  2013-04-02       Impact factor: 6.317

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