Literature DB >> 23973273

A methodology for extending domain coverage in SemRep.

Graciela Rosemblat1, Dongwook Shin, Halil Kilicoglu, Charles Sneiderman, Thomas C Rindflesch.   

Abstract

We describe a domain-independent methodology to extend SemRep coverage beyond the biomedical domain. SemRep, a natural language processing application originally designed for biomedical texts, uses the knowledge sources provided by the Unified Medical Language System (UMLS©). Ontological and terminological extensions to the system are needed in order to support other areas of knowledge. We extended SemRep's application by developing a semantic representation of a previously unsupported domain. This was achieved by adapting well-known ontology engineering phases and integrating them with the UMLS knowledge sources on which SemRep crucially depends. While the process to extend SemRep coverage has been successfully applied in earlier projects, this paper presents in detail the step-wise approach we followed and the mechanisms implemented. A case study in the field of medical informatics illustrates how the ontology engineering phases have been adapted for optimal integration with the UMLS. We provide qualitative and quantitative results, which indicate the validity and usefulness of our methodology. Published by Elsevier Inc.

Entities:  

Keywords:  Domain-independent ontology development methodology; Natural language processing application; Semantic predications; UMLS knowledge sources

Mesh:

Year:  2013        PMID: 23973273      PMCID: PMC3844019          DOI: 10.1016/j.jbi.2013.08.005

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


  18 in total

1.  Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.

Authors:  A R Aronson
Journal:  Proc AMIA Symp       Date:  2001

2.  The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text.

Authors:  Thomas C Rindflesch; Marcelo Fiszman
Journal:  J Biomed Inform       Date:  2003-12       Impact factor: 6.317

3.  Conceptualizing the world: lessons from history.

Authors:  Alexa T McCray
Journal:  J Biomed Inform       Date:  2005-09-28       Impact factor: 6.317

4.  Inductive creation of an annotation schema for manually indexing clinical conditions from emergency department reports.

Authors:  Wendy W Chapman; John N Dowling
Journal:  J Biomed Inform       Date:  2005-08-22       Impact factor: 6.317

5.  Methodology to develop and evaluate a semantic representation for NLP.

Authors:  Jeannie Y Irwin; Henk Harkema; Lee M Christensen; Titus Schleyer; Peter J Haug; Wendy W Chapman
Journal:  AMIA Annu Symp Proc       Date:  2009-11-14

Review 6.  A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men.

Authors:  Christopher M Miller; Thomas C Rindflesch; Marcelo Fiszman; Dimitar Hristovski; Dongwook Shin; Graciela Rosemblat; Han Zhang; Kingman P Strohl
Journal:  Sleep       Date:  2012-02-01       Impact factor: 5.849

7.  Discovering discovery patterns with Predication-based Semantic Indexing.

Authors:  Trevor Cohen; Dominic Widdows; Roger W Schvaneveldt; Peter Davies; Thomas C Rindflesch
Journal:  J Biomed Inform       Date:  2012-07-26       Impact factor: 6.317

8.  Word Sense Disambiguation by Selecting the Best Semantic Type Based on Journal Descriptor Indexing: Preliminary Experiment.

Authors:  Susanne M Humphrey; Willie J Rogers; Halil Kilicoglu; Dina Demner-Fushman; Thomas C Rindflesch
Journal:  J Am Soc Inf Sci Technol       Date:  2006-01-01

9.  Extending SemRep to the Public Health Domain.

Authors:  Graciela Rosemblat; Melissa P Resnick; Ione Auston; Dongwook Shin; Charles Sneiderman; Marcelo Fizsman; Thomas C Rindflesch
Journal:  J Am Soc Inf Sci Technol       Date:  2013-10

10.  Muscle Research and Gene Ontology: New standards for improved data integration.

Authors:  Erika Feltrin; Stefano Campanaro; Alexander D Diehl; Elisabeth Ehler; Georgine Faulkner; Jennifer Fordham; Chiara Gardin; Midori Harris; David Hill; Ralph Knoell; Paolo Laveder; Lorenza Mittempergher; Alessandra Nori; Carlo Reggiani; Vincenzo Sorrentino; Pompeo Volpe; Ivano Zara; Giorgio Valle; Jennifer Deegan
Journal:  BMC Med Genomics       Date:  2009-01-29       Impact factor: 3.063

View more
  5 in total

1.  Integrating Unified Medical Language System and Kleinberg's Burst Detection Algorithm into Research Topics of Medications for Post-Traumatic Stress Disorder.

Authors:  Shuang Xu; Dan Xu; Liang Wen; Chen Zhu; Ying Yang; Shuang Han; Peng Guan
Journal:  Drug Des Devel Ther       Date:  2020-09-24       Impact factor: 4.162

2.  Sortal anaphora resolution to enhance relation extraction from biomedical literature.

Authors:  Halil Kilicoglu; Graciela Rosemblat; Marcelo Fiszman; Thomas C Rindflesch
Journal:  BMC Bioinformatics       Date:  2016-04-14       Impact factor: 3.169

3.  Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT.

Authors:  Ferdinand Dhombres; Olivier Bodenreider
Journal:  J Biomed Semantics       Date:  2016-02-09

4.  Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature.

Authors:  Dalton Schutte; Jake Vasilakes; Anu Bompelli; Yuqi Zhou; Marcelo Fiszman; Hua Xu; Halil Kilicoglu; Jeffrey R Bishop; Terrence Adam; Rui Zhang
Journal:  J Biomed Inform       Date:  2022-06-13       Impact factor: 8.000

5.  Broad-coverage biomedical relation extraction with SemRep.

Authors:  Halil Kilicoglu; Graciela Rosemblat; Marcelo Fiszman; Dongwook Shin
Journal:  BMC Bioinformatics       Date:  2020-05-14       Impact factor: 3.169

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.