Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

被引:337
作者
Karp, Peter D. [1 ]
Paley, Suzanne M.
Krummenacker, Markus
Latendresse, Mario
Dale, Joseph M.
Lee, Thomas J.
Kaipa, Pallavi
Gilham, Fred
Spaulding, Aaron
Popescu, Liviu
Altman, Tomer
Paulsen, Ian [2 ]
Keseler, Ingrid M.
Caspi, Ron
机构
[1] SRI Int, Bioinformat Res Grp, Ctr Artificial Intelligence, Menlo Pk, CA 94025 USA
[2] Macquarie Univ, Sydney, NSW 2109, Australia
基金
美国国家卫生研究院;
关键词
Genome informatics; Metabolic pathways; Pathway bioinformatics; Model organism databases; Genome databases; Biological networks; Regulatory networks; ESCHERICHIA-COLI K-12; METABOLIC PATHWAYS; GENOMIC INFORMATION; GLOBAL PROPERTIES; GENE-REGULATION; DATABASE; MODEL; RESOURCE; VISUALIZATION; REACTOME;
D O I
10.1093/bib/bbp043
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry.
引用
收藏
页码:40 / 79
页数:40
相关论文
共 113 条
[1]  
ALASHQUR AM, 1989, VERY LARGE DATA BASES - PROCEEDINGS, P433
[2]  
[Anonymous], PATHEMA
[3]  
[Anonymous], 2004, GENOME BIOL
[4]   ApiDB: integrated resources for the apicomplexan bioinformatics resource center [J].
Aurrecoechea, Cristina ;
Heiges, Mark ;
Wang, Haiming ;
Wang, Zhiming ;
Fischer, Steve ;
Rhodes, Philippa ;
Miller, John ;
Kraemer, Eileen ;
Stoeckert, Christian J., Jr. ;
Roos, David S. ;
Kissinger, Jessica C. .
NUCLEIC ACIDS RESEARCH, 2007, 35 :D427-D430
[5]   PlasmoDB: a functional genomic database for malaria parasites [J].
Aurrecoechea, Cristina ;
Brestelli, John ;
Brunk, Brian P. ;
Dommer, Jennifer ;
Fischer, Steve ;
Gajria, Bindu ;
Gao, Xin ;
Gingle, Alan ;
Grant, Greg ;
Harb, Omar S. ;
Heiges, Mark ;
Innamorato, Frank ;
Iodice, John ;
Kissinger, Jessica C. ;
Kraemer, Eileen ;
Li, Wei ;
Miller, John A. ;
Nayak, Vishal ;
Pennington, Cary ;
Pinney, Deborah F. ;
Roos, David S. ;
Ross, Chris ;
Stoeckert, Christian J., Jr. ;
Treatman, Charles ;
Wang, Haiming .
NUCLEIC ACIDS RESEARCH, 2009, 37 :D539-D543
[6]  
BAIROCH A, 2009, UNIPROT KNOWLEDGEBAS
[7]   Integrating functional genomic information into the Saccharomyces genome database [J].
Ball, CA ;
Dolinski, K ;
Dwight, SS ;
Harris, MA ;
Issel-Tarver, L ;
Kasarskis, A ;
Scafe, CR ;
Sherlock, G ;
Binkley, G ;
Jin, H ;
Kaloper, M ;
Orr, SD ;
Schroeder, M ;
Weng, S ;
Zhu, Y ;
Botstein, D ;
Cherry, JM .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :77-80
[8]   CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks [J].
Baumbach, Jan .
BMC BIOINFORMATICS, 2007, 8
[9]  
*BIOCYC, BIOCYC COMP AN
[10]  
*BIOCYC, 2009, COMP BIOCYC DESKT MO