PubNet: a flexible system for visualizing literature derived networks

被引：25

作者：

Douglas, SM

Montelione, GT

Gerstein, M

机构：

[1] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

[2] Rutgers State Univ, Dept Mol Biol & Biochem, Ctr Adv Biotechnol & Med, Piscataway, NJ 08854 USA

[3] Robert Wood Johnson Med Sch, Piscataway, NJ 08854 USA

[4] Yale Univ, Dept Comp Sci, New Haven, CT 06520 USA

来源：

GENOME BIOLOGY | 2005年 / 6卷 / 09期

关键词：

D O I：

10.1186/gb-2005-6-9-r80

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 0836 [生物工程]; 090102 [作物遗传育种]; 100705 [微生物与生化药学];

摘要：

We have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors. This feature allows one to, for example, examine a literature derived network of genes based on functional similarity.

引用

页数：10

共 15 条

[1]

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium [J].

Acton, TB ;

Gunsalus, KC ;

Xiao, R ;

Ma, LC ;

Aramini, J ;

Baran, MC ;

Chiang, YW ;

Climent, T ;

Cooper, B ;

Denissova, NG ;

Douglas, SM ;

Everett, JK ;

Ho, CK ;

Macapagal, D ;

Rajan, PK ;

Shastry, R ;

Shih, LY ;

Swapna, GVT ;

Wilson, M ;

Wu, M ;

Gerstein, M ;

Inouye, M ;

Hunt, JF ;

Montelione, GT .

NUCLEAR MAGNETIC RESONANCE OF BIOLOGICAL MACROMOLECULES, PART C, 2005, 394 :210-243

[2]

ANDRADE MA, 1997, ISMB, V5, P25

[3]

PubMatrix: a tool for multiplex literature mining [J].

Becker, KG ;

Hosack, DA ;

Dennis, G ;

Lempicki, RA ;

Bright, TJ ;

Cheadle, C ;

Engel, J .

BMC BIOINFORMATICS, 2003, 4 (1)

[4]

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].

Boeckmann, B ;

Bairoch, A ;

Apweiler, R ;

Blatter, MC ;

Estreicher, A ;

Gasteiger, E ;

Martin, MJ ;

Michoud, K ;

O'Donovan, C ;

Phan, I ;

Pilbout, S ;

Schneider, M .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370

[5]

High-throughput computational and experimental techniques in structural genomics [J].

Chance, MR ;

Fiser, A ;

Sali, A ;

Pieper, U ;

Eswar, N ;

Xu, GP ;

Fajardo, JE ;

Radhakannan, T ;

Marinkovic, N .

GENOME RESEARCH, 2004, 14 (10B) :2145-2154

[6]

Content-rich biological network constructed by mining PubMed abstracts [J].

Chen, H ;

Sharp, BM .

BMC BIOINFORMATICS, 2004, 5 (1)

[7]

TargetDB: a target registration database for structural genomics projects [J].

Chen, L ;

Oughtred, R ;

Berman, HM ;

Westbrook, J .

BIOINFORMATICS, 2004, 20 (16) :2860-2862

[8]

A gene network for navigating the literature [J].

Hoffmann, R ;

Valencia, A .

NATURE GENETICS, 2004, 36 (07) :664-664

[9]

A literature network of human genes for high-throughput analysis of gene expression [J].

Jenssen, TK ;

Lægreid, A ;

Komorowski, J ;

Hovig, E .

NATURE GENETICS, 2001, 28 (01) :21-+

[10]

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline [J].

Lesley, SA ;

Kuhn, P ;

Godzik, A ;

Deacon, AM ;

Mathews, I ;

Kreusch, A ;

Spraggon, G ;

Klock, HE ;

McMullan, D ;

Shin, T ;

Vincent, J ;

Robb, A ;

Brinen, LS ;

Miller, MD ;

McPhillips, TM ;

Miller, MA ;

Scheibe, D ;

Canaves, JM ;

Guda, C ;

Jaroszewski, L ;

Selby, TL ;

Elsliger, MA ;

Wooley, J ;

Taylor, SS ;

Hodgson, KO ;

Wilson, IA ;

Schultz, PG ;

Stevens, RC .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (18) :11664-11669

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