PIMiner: a web tool for extraction of protein interactions from biomedical literature

被引：11

作者：

Chowdhary, Rajesh ^{[1
]}

Zhang, Jinfeng ^{[2
]}

Tan, Sin Lam ^{[3
]}

Osborne, Daniel E. ^{[2
]}

Bajic, Vladimir B. ^{[4
]}

Liu, Jun S. ^{[5
]}

机构：

[1] Marshfield Clin Fdn Med Res & Educ, MCRF, Biomed Informatifcs Res Ctr, Marshfield, WI 54449 USA

[2] Florida State Univ, Dept Stat, Tallahassee, FL 32306 USA

[3] Marshfield Clin Fdn Med Res & Educ, MCRF, Biomed Informat Res Ctr, Marshfield, WI 54449 USA

[4] King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia

[5] Harvard Univ, Dept Stat, Cambridge, MA 02138 USA

来源：

INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS | 2013年 / 7卷 / 04期

基金：

美国国家卫生研究院;

关键词：

PI; protein interactions; protein-protein interactions; literature mining; biological text-mining; systems biology; gene-protein networks; interactome mining; data mining; bioinformatics; complex biological networks; PREDICTION; GENE; INFORMATION;

D O I：

10.1504/IJDMB.2013.054232

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Information on Protein Interactions (PIs) is valuable for biomedical research, but often lies buried in the scientific literature and cannot be readily retrieved. While much progress has been made over the years in extracting PIs from the literature using computational methods, there is a lack of free, public, user-friendly tools for the discovery of PIs. We developed an online tool for the extraction of PI relationships from PubMed-abstracts, which we name PIMiner. Protein pairs and the words that describe their interactions are reported by PIMiner so that new interactions can be easily detected within text. The interaction likelihood levels are reported too. The option to extract only specific types of interactions is also provided. The PIMiner server can be accessed through a web browser or remotely through a client's command line. PIMiner can process 50,000 PubMed abstracts in approximately 7 min and thus appears suitable for large-scale processing of biological/biomedical literature.

引用

页码：450 / 462

页数：13

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