Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.

<h4>Background</h4>Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location o...

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Autores principales:	Rajesh Chowdhary, Sin Lam Tan, Jinfeng Zhang, Shreyas Karnik, Vladimir B Bajic, Jun S Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6b97bead1fea48468746c9a73352d119
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spelling	oai:doaj.org-article:6b97bead1fea48468746c9a73352d1192021-11-18T07:23:01ZContext-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.1932-620310.1371/journal.pone.0034480https://doaj.org/article/6b97bead1fea48468746c9a73352d1192012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22493694/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis.<h4>Results</h4>We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality.<h4>Conclusions</h4>CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/.Rajesh ChowdharySin Lam TanJinfeng ZhangShreyas KarnikVladimir B BajicJun S LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e34480 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rajesh Chowdhary Sin Lam Tan Jinfeng Zhang Shreyas Karnik Vladimir B Bajic Jun S Liu Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
description	<h4>Background</h4>Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis.<h4>Results</h4>We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality.<h4>Conclusions</h4>CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/.
format	article
author	Rajesh Chowdhary Sin Lam Tan Jinfeng Zhang Shreyas Karnik Vladimir B Bajic Jun S Liu
author_facet	Rajesh Chowdhary Sin Lam Tan Jinfeng Zhang Shreyas Karnik Vladimir B Bajic Jun S Liu
author_sort	Rajesh Chowdhary
title	Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
title_short	Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
title_full	Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
title_fullStr	Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
title_full_unstemmed	Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
title_sort	context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/6b97bead1fea48468746c9a73352d119
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Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.

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