Literature DB >> 19475725

The Neighborhood Auditing Tool: a hybrid interface for auditing the UMLS.

C Paul Morrey1, James Geller, Michael Halper, Yehoshua Perl.   

Abstract

The UMLS's integration of more than 100 source vocabularies, not necessarily consistent with one another, causes some inconsistencies. The purpose of auditing the UMLS is to detect such inconsistencies and to suggest how to resolve them while observing the requirement of fully representing the content of each source in the UMLS. A software tool, called the Neighborhood Auditing Tool (NAT), that facilitates UMLS auditing is presented. The NAT supports "neighborhood-based" auditing, where, at any given time, an auditor concentrates on a single-focus concept and one of a variety of neighborhoods of its closely related concepts. Typical diagrammatic displays of concept networks have a number of shortcomings, so the NAT utilizes a hybrid diagram/text interface that features stylized neighborhood views which retain some of the best features of both the diagrammatic layouts and text windows while avoiding the shortcomings. The NAT allows an auditor to display knowledge from both the Metathesaurus (concept) level and the Semantic Network (semantic type) level. Various additional features of the NAT that support the auditing process are described. The usefulness of the NAT is demonstrated through a group of case studies. Its impact is tested with a study involving a select group of auditors.

Entities:  

Mesh:

Year:  2009        PMID: 19475725      PMCID: PMC2891659          DOI: 10.1016/j.jbi.2009.01.006

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


  29 in total

1.  Discovering missed synonymy in a large concept-oriented Metathesaurus.

Authors:  W T Hole; S Srinivasan
Journal:  Proc AMIA Symp       Date:  2000

2.  Auditing the UMLS for redundant classifications.

Authors:  Yi Peng; Michael H Halper; Yehoshua Perl; James Geller
Journal:  Proc AMIA Symp       Date:  2002

3.  The Unified Medical Language System (UMLS): integrating biomedical terminology.

Authors:  Olivier Bodenreider
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  Auditing concept categorizations in the UMLS.

Authors:  Huanying Gu; Yehoshua Perl; Gai Elhanan; Hua Min; Li Zhang; Yi Peng
Journal:  Artif Intell Med       Date:  2004-05       Impact factor: 5.326

5.  Approaches to eliminating cycles in the UMLS Metathesaurus: naïve vs. formal.

Authors:  Fleur Mougin; Olivier Bodenreider
Journal:  AMIA Annu Symp Proc       Date:  2005

6.  Who is using the UMLS and how - insights from the UMLS user annual reports.

Authors:  Kin Wah Fung; William T Hole; Suresh Srinivasan
Journal:  AMIA Annu Symp Proc       Date:  2006

7.  Auditing as part of the terminology design life cycle.

Authors:  Hua Min; Yehoshua Perl; Yan Chen; Michael Halper; James Geller; Yue Wang
Journal:  J Am Med Inform Assoc       Date:  2006-08-23       Impact factor: 4.497

8.  The UMLS Metathesaurus: representing different views of biomedical concepts.

Authors:  P L Schuyler; W T Hole; M S Tuttle; D D Sherertz
Journal:  Bull Med Libr Assoc       Date:  1993-04

9.  The Unified Medical Language System.

Authors:  D A Lindberg; B L Humphreys; A T McCray
Journal:  Methods Inf Med       Date:  1993-08       Impact factor: 2.176

10.  Structural group-based auditing of missing hierarchical relationships in UMLS.

Authors:  Yan Chen; Huanying Helen Gu; Yehoshua Perl; James Geller
Journal:  J Biomed Inform       Date:  2008-08-20       Impact factor: 6.317

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  15 in total

1.  Auditing hierarchical cycles to locate other inconsistencies in the UMLS.

Authors:  Michael Halper; C Paul Morrey; Yan Chen; Gai Elhanan; George Hripcsak; Yehoshua Perl
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

2.  Validating UMLS Semantic Type Assignments Using SNOMED CT Semantic Tags.

Authors:  Huanying Gu; Zhe He; Duo Wei; Gai Elhanan; Yan Chen
Journal:  Methods Inf Med       Date:  2018-04-05       Impact factor: 2.176

3.  Expanding the extent of a UMLS semantic type via group neighborhood auditing.

Authors:  Yan Chen; Huanying Gu; Yehoshua Perl; Michael Halper; Junchuan Xu
Journal:  J Am Med Inform Assoc       Date:  2009-06-30       Impact factor: 4.497

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.  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

6.  Overcoming an obstacle in expanding a UMLS semantic type extent.

Authors:  Yan Chen; Huanying Gu; Yehoshua Perl; James Geller
Journal:  J Biomed Inform       Date:  2011-09-09       Impact factor: 6.317

7.  A study of terminology auditors' performance for UMLS semantic type assignments.

Authors:  Huanying Helen Gu; Gai Elhanan; Yehoshua Perl; George Hripcsak; James J Cimino; Julia Xu; Yan Chen; James Geller; C Paul Morrey
Journal:  J Biomed Inform       Date:  2012-06-09       Impact factor: 6.317

8.  Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.

Authors:  Zhe He; Yehoshua Perl; Gai Elhanan; Yan Chen; James Geller; Jiang Bian
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2017-12-18

9.  Logic-based assessment of the compatibility of UMLS ontology sources.

Authors:  Ernesto Jiménez-Ruiz; Bernardo Cuenca Grau; Ian Horrocks; Rafael Berlanga
Journal:  J Biomed Semantics       Date:  2011-03-07

10.  Visual comprehension and orientation into the COVID-19 CIDO ontology.

Authors:  Ling Zheng; Yehoshua Perl; Yongqun He; Christopher Ochs; James Geller; Hao Liu; Vipina K Keloth
Journal:  J Biomed Inform       Date:  2021-07-02       Impact factor: 8.000

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