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Automated text analysis of biomedical abstracts applied to the extraction of signaling pathways involved in plant cold-adaptation
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
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2006 (English)In: the Fifth International Conference on Bioinformatics of Genome Regulation and Structure: vol 3, Russian Academy of Sciences, 2006, 296-299 p.Conference paper, (Other academic)
Abstract [en]

Motivation: Automated text analysis is an important tool for facilitating the extraction of knowledge from biomedical abstracts, thereby enabling researchers to build pathway models that integrate and summarize information from a large number of sources. Advanced methods of in-depth analysis of texts using grammar-based approaches developed within the field of computational linguistics must be adapted to the special requirements and challenges posed by biomedical texts, so that these methods can be made available to the bioinformatics and computational biology communities. Results: Our system for automated text analysis and extraction of pathway information is here applied to a set of PubMed abstracts concerning the CBF signaling pathway, which is a key pathway involved in the cold-adaptation response of plants subjected to cold non-freezing temperatures. The system successfully and accurately re-discovers the main features of this pathway, while also pointing to interesting and plausible new hypotheses. The evaluation also reveals a number of issues which will be important targets in the continued development of the system, e.g. the need for an extended lexicon of taxonomic terms and an improved procedure for recognition of sentence boundaries.

Place, publisher, year, edition, pages
Russian Academy of Sciences, 2006. 296-299 p.
Identifiers
URN: urn:nbn:se:his:diva-1928ISI: 000243859500067ISBN: 5-7692-0848-1 OAI: oai:DiVA.org:his-1928DiVA: diva2:32204
Available from: 2007-09-21 Created: 2007-09-21 Last updated: 2013-03-19

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http://www.bionet.nsc.ru/meeting/bgrs2006/BGRS_2006_V3.pdf

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Gawronska, BarbaraOlsson, BjörnErlendsson, BjörnLindlöf, AngelicaDura, Elzbieta
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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
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More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
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  • asciidoc
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