Skip to main content

Natural Language Processing

  • Reference work entry

Synonyms

Biomedical natural language processing (BioNLP); Computational linguistics; Information extraction; Natural language understanding; Text mining; Text processing

Definition

Natural language processing is the analysis of linguistic data, most commonly in the form of textual data such as documents or publications, using computational methods. The goal of natural language processing is generally to build a representation of the text that adds structure to the unstructured natural language, by taking advantage of insights from linguistics. This structure can be syntactic in nature, capturing the grammatical relationships among constituents of the text, or more semantic, capturing the meaning conveyed by the text.

Natural language processing is used in systems biology to develop applications that integrate information extracted from the literature with other sources of biological data (see Applied Text Mining).

Characteristics

The typical natural language processing system consists...

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   899.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   549.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Cohen KB, Verspoor K, Johnson H, Roeder C, Ogren P, Baumgartner W Jr., White E, Tipney H, Hunter L (2011) High-precision biological event extraction: Effects of system and data. Comput Intell 27(4)

    Google Scholar 

  • Dai H-J, Lai P-T, Tsai RT-H (2010) Multistage gene normalization and svm-based ranking for protein interactor extraction in full-text articles. IEEE/ACM Trans Comput Biol Bioinformatics 7(3):412–420

    CAS  Google Scholar 

  • Ferrucci D, Lally A, Verspoor K (eds) (2009) Unstructured information management architecture (UIMA) Version 1.0. OASIS Standard, 2 Mar 2009

    Google Scholar 

  • Hakenberg J, Leaman R, Ha Vo N, Jonnalagadda S, Sullivan R, Miller C, Tari L, Baral C, Gonzalez G (2010) Efficient extraction of protein–protein interactions from full-text articles. IEEE/ACM Trans Comput Biol Bioinformatics 7(3):481–494

    CAS  Google Scholar 

  • Hirschman L, Yeh A, Blaschke C, Valencia A (2005) Overview of biocreative: critical assessment of information extraction for biology. BMC Bioinformatics 6(Suppl 1):S1

    PubMed  Google Scholar 

  • Hunter L, Bretonnel Cohen K (2006) Biomedical language processing: what’s beyond PubMed? Mol Cell 21:589–594

    PubMed  CAS  Google Scholar 

  • Kim J-D, Ohta T, Pyysalo S, Kano Y, Tsujii J (2009) Overview of BioNLP’09 shared task on event extraction. In: Proceedings of the Workshop on BioNLP: Shared Task, Association for Computational Linguistics, Boulder, Colorado, pp 1–9

    Google Scholar 

  • Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A (2008) Evaluation of text-mining systems for biology: overview of the second BioCreative community challenge. Genome Biol 9(Suppl 2):S1

    PubMed  Google Scholar 

  • Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A (2010) The FEBS letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol 28:897–899

    PubMed  CAS  Google Scholar 

  • Nakov P, Schwartz A, Wolf B, Hearst M (2005) Supporting annotation layers for natural language processing. In: ACL 2005 Poster/Demo Track, Ann Arbor

    Google Scholar 

  • Porter MF (1980) An algorithm for suffix stripping. Program 14(3):130–137

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Karin Verspoor .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this entry

Cite this entry

Verspoor, K., Cohen, K.B. (2013). Natural Language Processing. In: Dubitzky, W., Wolkenhauer, O., Cho, KH., Yokota, H. (eds) Encyclopedia of Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-9863-7_158

Download citation

Publish with us

Policies and ethics