Literature DB >> 14764611

An enriched unified medical language system semantic network with a multiple subsumption hierarchy.

Li Zhang1, Yehoshua Perl, Michael Halper, James Geller, James J Cimino.   

Abstract

OBJECTIVE: The Unified Medical Language System's (UMLS's) Semantic Network's (SN's) two-tree structure is restrictive because it does not allow a semantic type to be a specialization of several other semantic types. In this article, the SN is expanded into a multiple subsumption structure with a directed acyclic graph (DAG) IS-A hierarchy, allowing a semantic type to have multiple parents. New viable IS-A links are added as warranted.
DESIGN: Two methodologies are presented to identify and add new viable IS-A links. The first methodology is based on imposing the characteristic of connectivity on a previously presented partition of the SN. Four transformations are provided to find viable IS-A links in the process of converting the partition's disconnected groups into connected ones. The second methodology identifies new IS-A links through a string matching process involving names and definitions of various semantic types in the SN. A domain expert is needed to review all the results to determine the validity of the new IS-A links.
RESULTS: Nineteen new IS-A links are added to the SN, and four new semantic types are also created to support the multiple subsumption framework. The resulting network, called the Enriched Semantic Network (ESN), exhibits a DAG-structured hierarchy. A partition of the ESN containing 19 connected groups is also derived.
CONCLUSION: The ESN is an expanded abstraction of the UMLS compared with the original SN. Its multiple subsumption hierarchy can accommodate semantic types with multiple parents. Its representation thus provides direct access to a broader range of subsumption knowledge.

Entities:  

Mesh:

Year:  2004        PMID: 14764611      PMCID: PMC400518          DOI: 10.1197/jamia.M1269

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


  18 in total

1.  Building cross-thesauri with the support of UMLS.

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Journal:  Stud Health Technol Inform       Date:  1998

2.  Aggregating UMLS semantic types for reducing conceptual complexity.

Authors:  A T McCray; A Burgun; O Bodenreider
Journal:  Stud Health Technol Inform       Date:  2001

3.  The cohesive metaschema: a higher-level abstraction of the UMLS Semantic Network.

Authors:  Yehoshua Perl; Zong Chen; Michael Halper; James Geller; Li Zhang; Yi Peng
Journal:  J Biomed Inform       Date:  2002-06       Impact factor: 6.317

4.  Scale and context: issues in ontologies to link health- and bio-informatics.

Authors:  Alan L Rector; Jeremy Rogers; Angus Roberts; Chris Wroe
Journal:  Proc AMIA Symp       Date:  2002

5.  Auditing the UMLS for redundant classifications.

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

6.  Partitioning the UMLS semantic network.

Authors:  Zong Chen; Yehoshua Perl; Michael Halper; James Geller; Huanying Gu
Journal:  IEEE Trans Inf Technol Biomed       Date:  2002-06

7.  Designing metaschemas for the UMLS enriched semantic network.

Authors:  Li Zhang; Yehoshua Perl; Michael Halper; James Geller
Journal:  J Biomed Inform       Date:  2003-12       Impact factor: 6.317

8.  The representation of meaning in the UMLS.

Authors:  A T McCray; S J Nelson
Journal:  Methods Inf Med       Date:  1995-03       Impact factor: 2.176

9.  A logical foundation for representation of clinical data.

Authors:  K E Campbell; A K Das; M A Musen
Journal:  J Am Med Inform Assoc       Date:  1994 May-Jun       Impact factor: 4.497

10.  Lexical methods for managing variation in biomedical terminologies.

Authors:  A T McCray; S Srinivasan; A C Browne
Journal:  Proc Annu Symp Comput Appl Med Care       Date:  1994
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  11 in total

1.  Relationship structures and semantic type assignments of the UMLS Enriched Semantic Network.

Authors:  Li Zhang; Michael Halper; Yehoshua Perl; James Geller; James J Cimino
Journal:  J Am Med Inform Assoc       Date:  2005-07-27       Impact factor: 4.497

2.  SemCat: semantically categorized entities for genomics.

Authors:  Lorraine Tanabe; Lynne H Thom; Wayne Matten; Donald C Comeau; W John Wilbur
Journal:  AMIA Annu Symp Proc       Date:  2006

Review 3.  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

4.  Updating the genomic component of the UMLS Semantic Network.

Authors:  Barry Cohen; Yan Chen; Yehoshua Perl
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

5.  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

6.  Using Convolutional Neural Networks to Support Insertion of New Concepts into SNOMED CT.

Authors:  Hao Liu; James Geller; Michael Halper; Yehoshua Perl
Journal:  AMIA Annu Symp Proc       Date:  2018-12-05

Review 7.  Abstraction networks for terminologies: Supporting management of "big knowledge".

Authors:  Michael Halper; Huanying Gu; Yehoshua Perl; Christopher Ochs
Journal:  Artif Intell Med       Date:  2015-04-02       Impact factor: 5.326

8.  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

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

Authors:  C Paul Morrey; James Geller; Michael Halper; Yehoshua Perl
Journal:  J Biomed Inform       Date:  2009-06       Impact factor: 6.317

10.  A chemical specialty semantic network for the Unified Medical Language System.

Authors:  C Paul Morrey; Yehoshua Perl; Michael Halper; Ling Chen; Huanying Helen Gu
Journal:  J Cheminform       Date:  2012-05-11       Impact factor: 5.514

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