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. 2013;7(4):450-62.
doi: 10.1504/ijdmb.2013.054232.

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

Rajesh Chowdhary  1 , Jinfeng Zhang, Sin Lam Tan, Daniel E Osborne, Vladimir B Bajic, Jun S Liu
Affiliations

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

Rajesh Chowdhary et al. Int J Data Min Bioinform. 2013.

Abstract

Information on Protein Interactions (Pls) 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 Pls from the literature using computational methods, there is a lack of free, public, user-friendly tools for the discovery of Pls. 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.

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Figures

Figure 1
Figure 1
Web interface of PIMiner Modules A and B
Figure 2
Figure 2
Workflow of PIMiner Modules A and B
Figure 3
Figure 3
Typical output from PIMiner. The PI triplet is shown highlighted in colour with red indicating the target protein pair and purple indicating the interaction word
See this image and copyright information in PMC

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