Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users.

Bioinformatics
Hagit ShatkayW John Wilbur

Abstract

Much current research in biomedical text mining is concerned with serving biologists by extracting certain information from scientific text. We note that there is no 'average biologist' client; different users have distinct needs. For instance, as noted in past evaluation efforts (BioCreative, TREC, KDD) database curators are often interested in sentences showing experimental evidence and methods. Conversely, lab scientists searching for known information about a protein may seek facts, typically stated with high confidence. Text-mining systems can target specific end-users and become more effective, if the system can first identify text regions rich in the type of scientific content that is of interest to the user, retrieve documents that have many such regions, and focus on fact extraction from these regions. Here, we study the ability to characterize and classify such text automatically. We have recently introduced a multi-dimensional categorization and annotation scheme, developed to be applicable to a wide variety of biomedical documents and scientific statements, while intended to support specific biomedical retrieval and extraction tasks. The annotation scheme was applied to a large corpus in a controlled effort by eight...Continue Reading

References

Aug 10, 2002·Bioinformatics·Michael KrauthammerAndrey Rzhetsky
Aug 15, 2002·Bioinformatics·Lorraine Tanabe, W John Wilbur
Jul 31, 2003·Nucleic Acids Research·Soumya RaychaudhuriRuss B Altman
Apr 10, 2004·Bioinformatics·L SmithW J Wilbur
Jul 7, 2005·Genome Biology·Martin Krallinger, Alfonso Valencia
Oct 11, 2005·Briefings in Bioinformatics·Hagit Shatkay

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Citations

Oct 27, 2009·BMC Bioinformatics·Paul ThompsonSophia Ananiadou
Feb 26, 2010·BMC Bioinformatics·J Lynn FinkPhilip E Bourne
May 25, 2011·BMC Bioinformatics·Rashmi PrasadHong Yu
Oct 12, 2011·BMC Bioinformatics·Paul ThompsonSophia Ananiadou
Jun 17, 2011·BMC Bioinformatics·Rezarta Islamaj DoğanZhiyong Lu
May 25, 2012·BMC Bioinformatics·Makoto MiwaSophia Ananiadou
Jan 28, 2012·BMC Bioinformatics·Ruihua FangPaul W Sternberg
Jan 18, 2013·BMC Bioinformatics·Raheel NawazSophia Ananiadou
May 23, 2009·PLoS Computational Biology·Andrey RzhetskyW John Wilbur
Dec 31, 2009·PLoS Computational Biology·Raul Rodriguez-Esteban
Jan 21, 2011·PloS One·Daehyun Kim, Hong Yu
Feb 18, 2014·Journal of Biomedical Informatics·Hamed HassanzadehJane Hunter
Jun 8, 2014·Briefings in Functional Genomics·Sophia AnaniadouDouglas B Kell
Aug 17, 2010·Journal of Biomedical Informatics·Shashank Agarwal, Hong Yu
Jan 20, 2012·Healthcare Informatics Research·Mi Hwa SongYoung Ho Lee
May 7, 2013·Biomedical Informatics Insights·Tudor GrozaJane Hunter
Oct 16, 2016·F1000Research·Jonathan P TennantChris H J Hartgerink
Jun 22, 2017·Briefings in Bioinformatics·Halil Kilicoglu
Mar 23, 2021·Computers & Industrial Engineering·Houssein DhayneYehia Taher
Aug 21, 2021·AJNR. American Journal of Neuroradiology·F LiuM P Rosen

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Software Mentioned

Google Scholar
BioCreative
MedPost
YamCha
LibSVM

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