Extracting interactions between proteins from the literature

Deyu Zhou; Yulan He

doi:10.1016/j.jbi.2007.11.008

Extracting interactions between proteins from the literature

Deyu Zhou, Yulan He

Computer Science Research Group

Research output: Contribution to journal › Article › peer-review

Abstract

During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a outline of the various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions. It surveys methodologies involved in plain texts analyzing and processing, categorizes current work in biomedical information extraction, and provides examples of these methods. Challenges in the field are also presented and possible solutions are discussed.

Original language	English
Pages (from-to)	393-407
Number of pages	15
Journal	Journal of Biomedical Informatics
Volume	41
Issue number	2
DOIs	https://doi.org/10.1016/j.jbi.2007.11.008
Publication status	Published - Apr 2008

Bibliographical note

NOTICE: this is the author’s version of a work that was accepted for publication in Journal of biomedical informatics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Zhou, D & He, Y 2008, 'Extracting interactions between proteins from the literature' Journal of biomedical informatics, vol. 41, no. 2 (2008) DOI http://dx.doi.org/10.1016/j.jbi.2007.11.008.

Access to Document

10.1016/j.jbi.2007.11.008

Extracting Interactions between proteins
NOTICE: this is the author’s version of a work that was accepted for publication in Journal of biomedical informatics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Zhou, D & He, Y 2008, 'Extracting interactions between proteins from the literature' Journal of biomedical informatics, vol. 41, no. 2 (2008) DOI http://dx.doi.org/10.1016/j.jbi.2007.11.008.
Accepted author manuscript, 313 KB

Cite this

@article{c2c299ba74c64204aac9adcf7a819662,

title = "Extracting interactions between proteins from the literature",

abstract = "During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a outline of the various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions. It surveys methodologies involved in plain texts analyzing and processing, categorizes current work in biomedical information extraction, and provides examples of these methods. Challenges in the field are also presented and possible solutions are discussed.",

author = "Deyu Zhou and Yulan He",

note = "NOTICE: this is the author{\textquoteright}s version of a work that was accepted for publication in Journal of biomedical informatics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Zhou, D & He, Y 2008, 'Extracting interactions between proteins from the literature' Journal of biomedical informatics, vol. 41, no. 2 (2008) DOI http://dx.doi.org/10.1016/j.jbi.2007.11.008.",

year = "2008",

month = apr,

doi = "10.1016/j.jbi.2007.11.008",

language = "English",

volume = "41",

pages = "393--407",

journal = "Journal of Biomedical Informatics",

issn = "1532-0464",

publisher = "Academic Press Inc.",

number = "2",

}

TY - JOUR

T1 - Extracting interactions between proteins from the literature

AU - Zhou, Deyu

AU - He, Yulan

N1 - NOTICE: this is the author’s version of a work that was accepted for publication in Journal of biomedical informatics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Zhou, D & He, Y 2008, 'Extracting interactions between proteins from the literature' Journal of biomedical informatics, vol. 41, no. 2 (2008) DOI http://dx.doi.org/10.1016/j.jbi.2007.11.008.

PY - 2008/4

Y1 - 2008/4

N2 - During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a outline of the various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions. It surveys methodologies involved in plain texts analyzing and processing, categorizes current work in biomedical information extraction, and provides examples of these methods. Challenges in the field are also presented and possible solutions are discussed.

AB - During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a outline of the various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions. It surveys methodologies involved in plain texts analyzing and processing, categorizes current work in biomedical information extraction, and provides examples of these methods. Challenges in the field are also presented and possible solutions are discussed.

UR - http://www.scopus.com/inward/record.url?scp=40049083982&partnerID=8YFLogxK

U2 - 10.1016/j.jbi.2007.11.008

DO - 10.1016/j.jbi.2007.11.008

M3 - Article

AN - SCOPUS:40049083982

SN - 1532-0464

VL - 41

SP - 393

EP - 407

JO - Journal of Biomedical Informatics

JF - Journal of Biomedical Informatics

IS - 2

ER -

Extracting interactions between proteins from the literature

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this