Literature DB >> 20351894

UMLS-Interface and UMLS-Similarity : open source software for measuring paths and semantic similarity.

Bridget T McInnes1, Ted Pedersen, Serguei V S Pakhomov.   

Abstract

A number of computational measures for determining semantic similarity between pairs of biomedical concepts have been developed using various standards and programming platforms. In this paper, we introduce two new open-source frameworks based on the Unified Medical Language System (UMLS). These frameworks consist of the UMLS-Similarity and UMLS-Interface packages. UMLS-Interface provides path information about UMLS concepts. UMLS-Similarity calculates the semantic similarity between UMLS concepts using several previously developed measures and can be extended to include new measures. We validate the functionality of these frameworks by reproducing the results from previous work. Our frameworks constitute a significant contribution to the field of biomedical Natural Language Processing by providing a common development and testing platform for semantic similarity measures based on the UMLS.

Mesh：

Year:  2009        PMID： 20351894      PMCID： PMC2815481     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN： 1559-4076


  9 in total

1.  Semantic similarity measures as tools for exploring the gene ontology.

Authors:  P W Lord; R D Stevens; A Brass; C A Goble
Journal:  Pac Symp Biocomput       Date:  2003

2.  Towards the development of a conceptual distance metric for the UMLS.

Authors:  Jorge E Caviedes; James J Cimino
Journal:  J Biomed Inform       Date:  2004-04       Impact factor: 6.317

3.  Aligning knowledge sources in the UMLS: methods, quantitative results, and applications.

Authors:  Olivier Bodenreider; Anita Burgun
Journal:  Stud Health Technol Inform       Date:  2004

4.  Measures of semantic similarity and relatedness in the biomedical domain.

Authors:  Ted Pedersen; Serguei V S Pakhomov; Siddharth Patwardhan; Christopher G Chute
Journal:  J Biomed Inform       Date:  2006-06-10       Impact factor: 6.317

5.  A cluster-based approach for semantic similarity in the biomedical domain.

Authors:  Hisham Al-Mubaid; Hoa A Nguyen
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2006

6.  A document clustering and ranking system for exploring MEDLINE citations.

Authors:  Yongjing Lin; Wenyuan Li; Keke Chen; Ying Liu
Journal:  J Am Med Inform Assoc       Date:  2007-06-28       Impact factor: 4.497

7.  Comparison of ontology-based semantic-similarity measures.

Authors:  Wei-Nchih Lee; Nigam Shah; Karanjot Sundlass; Mark Musen
Journal:  AMIA Annu Symp Proc       Date:  2008-11-06

8.  UMLS-Query: a perl module for querying the UMLS.

Authors:  Nigam H Shah; Nigam Shah; Mark A Muse; Mark Musen
Journal:  AMIA Annu Symp Proc       Date:  2008-11-06

9.  Inter-patient distance metrics using SNOMED CT defining relationships.

Authors:  Genevieve B Melton; Simon Parsons; Frances P Morrison; Adam S Rothschild; Marianthi Markatou; George Hripcsak
Journal:  J Biomed Inform       Date:  2006-02-24       Impact factor: 6.317
  9 in total
  51 in total

1.  Knowledge-based method for determining the meaning of ambiguous biomedical terms using information content measures of similarity.

Authors:  Bridget T McInnes; Ted Pedersen; Ying Liu; Genevieve B Melton; Serguei V Pakhomov
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

2.  k-Neighborhood decentralization: a comprehensive solution to index the UMLS for large scale knowledge discovery.

Authors:  Yang Xiang; Kewei Lu; Stephen L James; Tara B Borlawsky; Kun Huang; Philip R O Payne
Journal:  J Biomed Inform       Date:  2011-12-02       Impact factor: 6.317

3.  A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts.

Authors:  Rimma Pivovarov; Noémie Elhadad
Journal:  J Biomed Inform       Date:  2012-01-25       Impact factor: 6.317

4.  A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources.

Authors:  Sungrim Moon; Serguei Pakhomov; Nathan Liu; James O Ryan; Genevieve B Melton
Journal:  J Am Med Inform Assoc       Date:  2013-06-27       Impact factor: 4.497

5.  Towards a framework for developing semantic relatedness reference standards.

Authors:  Serguei V S Pakhomov; Ted Pedersen; Bridget McInnes; Genevieve B Melton; Alexander Ruggieri; Christopher G Chute
Journal:  J Biomed Inform       Date:  2010-10-31       Impact factor: 6.317

6.  Semantic Similarity and Relatedness between Clinical Terms: An Experimental Study.

Authors:  Serguei Pakhomov; Bridget McInnes; Terrence Adam; Ying Liu; Ted Pedersen; Genevieve B Melton
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

7.  The support of human genetic evidence for approved drug indications.

Authors:  Matthew R Nelson; Hannah Tipney; Jeffery L Painter; Judong Shen; Paola Nicoletti; Yufeng Shen; Aris Floratos; Pak Chung Sham; Mulin Jun Li; Junwen Wang; Lon R Cardon; John C Whittaker; Philippe Sanseau
Journal:  Nat Genet       Date:  2015-06-29       Impact factor: 38.330

8.  U-path: An undirected path-based measure of semantic similarity.

Authors:  Bridget T McInnes; Ted Pedersen; Ying Liu; Genevieve B Melton; Serguei V Pakhomov
Journal:  AMIA Annu Symp Proc       Date:  2014-11-14

9.  A study of active learning methods for named entity recognition in clinical text.

Authors:  Yukun Chen; Thomas A Lasko; Qiaozhu Mei; Joshua C Denny; Hua Xu
Journal:  J Biomed Inform       Date:  2015-09-15       Impact factor: 6.317

10.  Incorporating expert terminology and disease risk factors into consumer health vocabularies.

Authors:  Michael Seedorff; Kevin J Peterson; Laurie A Nelsen; Cristian Cocos; Jennifer B McCormick; Christopher G Chute; Jyotishman Pathak
Journal:  Pac Symp Biocomput       Date:  2013
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