BioNLP: Biomedical Text Mining

K. Bretonnel Cohen

Biomedical natural language processing possesses unique challenges and presents unique opportunities that make it a hot topic of interest in natural language processing. This chapter examines them.

Bibtex Citation

  @incollection{cohen-handbook10,
   author = {K. Bretonnel Cohen},
   title = {{BioNLP:} Biomedical Text Mining},
   booktitle = {Handbook of Natural Language Processing, Second Edition},
   editor = {Nitin Indurkhya and Fred J. Damerau},
   publisher = {CRC Press, Taylor and Francis Group},
   address = {Boca Raton, FL},
   year = {2010},
   note = {ISBN 978-1420085921}
  }

Online Resources

Corpora for biomedical NLP

http://compbio.uchsc.edu/ccp/corpora/obtaining.shtml

Bibliographies of BioNLP

http://blimp.cs.queensu.ca/index.html BLIMP (Biomedical Literature (and text) Mining Publications

LingPipe code base for biomedical and other NLP

http://alias-i.com/lingpipe/

A biomedical tokenizer optimized for information retrieval

http://sifaka.cs.uiuc.edu/jiang4/software/BioTokenization.html

Code base for maintaining MEDLINE in a local relational database

http://biotext.berkeley.edu/software.html