Literature DB >> 18314582

Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).

John D Osborne1, Simon Lin, Lihua Zhu, Warren A Kibbe.   

Abstract

Detailed instruction is described for mapping unstructured, free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Transfer (MMTx). MMTx can be used in applications including mining and inferring relationship between concepts in MEDLINE publications by transforming free text into computable concepts. MMTx is in general not designed to be an end-user program; therefore, a simple analysis is described using MMTx for users without any programming knowledge. In addition, two Java template files are provided for automated processing of the output from MMTx and users can adopt this with minimum Java program experience.

Entities:  

Mesh：

Year:  2007        PMID： 18314582     DOI： 10.1007/978-1-59745-547-3_9

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  9 in total

1.  Interactive Cohort Identification of Sleep Disorder Patients Using Natural Language Processing and i2b2.

Authors:  W Chen; R Kowatch; S Lin; M Splaingard; Y Huang
Journal:  Appl Clin Inform       Date:  2015-05-27       Impact factor: 2.342

2.  Application of clinical text data for phenome-wide association studies (PheWASs).

Authors:  Scott J Hebbring; Majid Rastegar-Mojarad; Zhan Ye; John Mayer; Crystal Jacobson; Simon Lin
Journal:  Bioinformatics       Date:  2015-02-04       Impact factor: 6.937

3.  An exploratory study of user-centered indexing of published biomedical images.

Authors:  Sujin Kim
Journal:  J Med Libr Assoc       Date:  2013-01

4.  Chapter 15: disease gene prioritization.

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Journal:  PLoS Comput Biol       Date:  2013-04-25       Impact factor: 4.475

5.  Disease Ontology: a backbone for disease semantic integration.

Authors:  Lynn Marie Schriml; Cesar Arze; Suvarna Nadendla; Yu-Wei Wayne Chang; Mark Mazaitis; Victor Felix; Gang Feng; Warren Alden Kibbe
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6.  Comparing clinical quality indicators for asthma management in children with outcome measures used in randomised controlled trials: a protocol.

Authors:  Miew Keen Choong; Guy Tsafnat; Peter Hibbert; William B Runciman; Enrico Coiera
Journal:  BMJ Open       Date:  2015-09-08       Impact factor: 2.692

7.  A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records.

Authors:  Li Jiang; Stefan M Edwards; Bo Thomsen; Christopher T Workman; Bernt Guldbrandtsen; Peter Sørensen
Journal:  BMC Bioinformatics       Date:  2014-09-24       Impact factor: 3.169

8.  Linking clinical quality indicators to research evidence - a case study in asthma management for children.

Authors:  Miew Keen Choong; Guy Tsafnat; Peter Hibbert; William B Runciman; Enrico Coiera
Journal:  BMC Health Serv Res       Date:  2017-07-21       Impact factor: 2.655

9.  A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers.

Authors:  Nathan P Palmer; Patrick R Schmid; Bonnie Berger; Isaac S Kohane
Journal:  Genome Biol       Date:  2012-08-21       Impact factor: 13.583
  9 in total

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