World Library  
Flag as Inappropriate
Email this Article

Biomedical text mining

Article Id: WHEBN0002948178
Reproduction Date:

Title: Biomedical text mining  
Author: World Heritage Encyclopedia
Language: English
Subject: FACTA, Anne O'Tate, Data mining, PubGene, Biovista
Collection: Bioinformatics, Data Mining
Publisher: World Heritage Encyclopedia

Biomedical text mining

Biomedical text mining (also known as BioNLP) refers to text mining applied to texts and literature of the biomedical and molecular biology domain. It is a rather recent research field on the edge of natural language processing, bioinformatics, medical informatics and computational linguistics.

There is an increasing interest in text mining and information extraction strategies applied to the biomedical and molecular biology literature due to the increasing number of electronically available publications stored in databases such as PubMed.


  • Main applications 1
  • Conferences at which BioNLP research is presented 2
  • See also 3
  • External links 4
  • References 5
  • Further reading 6

Main applications

The main developments in this area have been related to the identification of biological entities (named entity recognition), such as protein and gene names as well as chemical compounds and drugs [1] in free text, the association of gene clusters obtained by microarray experiments with the biological context provided by the corresponding literature, automatic extraction of protein interactions and associations of proteins to functional concepts (e.g. gene ontology terms). Even the extraction of kinetic parameters from text or the subcellular location of proteins have been addressed by information extraction and text mining technology. Information extraction and text mining methods have been explored to extract information related to biological processes and diseases.[2]

Conferences at which BioNLP research is presented

BioNLP is presented at a variety of meetings:

See also

External links

  • Bio-NLP resources, systems and application database collection
  • The BioNLP mailing list archives
  • Corpora for biomedical text mining
  • The BioCreative evaluations of biomedical text mining technologies
  • Directory of people involved in BioNLP


  1. ^ M Krallinger, F Leitner, O Rabal, M Vazquez, J Oyarzabal and A Valencia, Overview of the chemical compound and drug name recognition (CHEMDNER) task. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop vol. 2. 6-37.
  2. ^ Krallinger, M; Leitner, F; Valencia, A (2010). "Analysis of Biological Processes and Diseases Using Text Mining Approaches". Bioinformatics Methods in Clinical Research. Methods in Molecular Biology 593. pp. 341–82.  

Further reading

  • Krallinger M, Valencia A (2005). "Text-mining and information-retrieval services for molecular biology". Genome Biol. 6 (7): 224.  
  • Hoffmann R, Krallinger M, Andres E, Tamames J, Blaschke C, Valencia A (May 2005). "Text mining for metabolic pathways, signaling cascades, and protein networks". Sci. STKE 2005 (283): pe21.  
  • Krallinger M, Erhardt RA, Valencia A (March 2005). "Text-mining approaches in molecular biology and biomedicine". Drug Discov. Today 10 (6): 439–45.  
  • Biomedical Literature Mining Publications (BLIMP): A comprehensive and regularly updated index of publications on (bio)medical text mining
This article was sourced from Creative Commons Attribution-ShareAlike License; additional terms may apply. World Heritage Encyclopedia content is assembled from numerous content providers, Open Access Publishing, and in compliance with The Fair Access to Science and Technology Research Act (FASTR), Wikimedia Foundation, Inc., Public Library of Science, The Encyclopedia of Life, Open Book Publishers (OBP), PubMed, U.S. National Library of Medicine, National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health (NIH), U.S. Department of Health & Human Services, and, which sources content from all federal, state, local, tribal, and territorial government publication portals (.gov, .mil, .edu). Funding for and content contributors is made possible from the U.S. Congress, E-Government Act of 2002.
Crowd sourced content that is contributed to World Heritage Encyclopedia is peer reviewed and edited by our editorial staff to ensure quality scholarly research articles.
By using this site, you agree to the Terms of Use and Privacy Policy. World Heritage Encyclopedia™ is a registered trademark of the World Public Library Association, a non-profit organization.

Copyright © World Library Foundation. All rights reserved. eBooks from Project Gutenberg are sponsored by the World Library Foundation,
a 501c(4) Member's Support Non-Profit Organization, and is NOT affiliated with any governmental agency or department.