The Pathway Tools software

By Peter D. Karp, Suzanne M. Paley, Pedro Romero. Intelligent Systems in Molecular Biology, 2002

691 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/32b5f303d01ff37cdfaa1a7754d76ae50748a93e

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Citations in the corpus

AraCyc: A Biochemical Pathway Database for Arabidopsis1 (2003, methodology): “In this work, we used Pathway Tools software (Karp et al., 2002a) to build a database for Arabidopsis metabolism .”
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms (2004, methodology): “Using the MetaCyc Database of metabolic reactions (7) and the Pathway Tools software created by Peter Karp’s group (8) The Find Chromosomal Features search provides advanced options for ﬁnding a gene or genes based on one or more criteria, including feature type (e.g. ORF, tRNA); protein molecular…”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “To address this shortcoming, PATHOLOGIC, the metabolic network reconstruction software tied to the BioCyc metabolic databases, includes an algorithm performing the identification of gene-reaction links from textual annotations (Karp et al., 2002) (see Table 3).”
A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, methodology): “Software tools such as Pathway tools 30 or metaSHARK 31 can be used for the generation of draft reconstruction, but they do not replace the manual curation.”
Gut microbiome based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease (2017, neutral): “(Karp et al., 2002) ORFs were generated from assembled contigs and unassembled singleton reads using MetaGene (Noguchi et al., 2006).”
The genome of the blood fluke Schistosoma mansoni (2009, positive): “An S. mansoni metabolic pathways database, SchistoCyc (http://schistocyc.schistodb.net/ptools), was created using the Pathway Tools software 83 , which contains algorithms to predict an organism’s metabolic pathways from its genome by comparison to MetaCyc, a reference pathways database 84 .”
MetaCyc: a multiorganism database of metabolic pathways and enzymes (2005, methodology): “An initial motivation for creating MetaCyc (1), a multiorganism database (DB) of metabolic pathways and enzymes, was to provide a reference database to be used in conjunction with SRI International’s (SRI’s) Pathway Tools software ( 2 ) to computationally predict the metabolic pathway complement of ”
MaGe: a microbial genome annotation system supported by synteny results (2006, methodology): “However, we plan to improve some decision rules, mainly by introducing data from predicted metabolic pathways obtained with the BioCyc software ( 46 ,47), and by combining co-localization results with phylogenetic profiles.”
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases (2007, background): “Fatty Acid and Lipids Degradation (18) Alcohols Degradation (14) Hormones Degradation ( 15 ) Aldehyde Degradation (12) Nucleosides and Nucleotides Degradation and Recycling (9)”
Maize Metabolic Network Construction and Transcriptome Analysis (2013, methodology): “We provide a short MaizeCyc tutorial (Supplemental File S1) aimed at new users on how to browse, search, and use tools such as the OMICS viewer (Karp et al., 2002) (Supplemental Fig.”
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, background): “of unknown biological and chemical pathways in all organisms, pathways for unexplored organisms can be predicted using PathoLogic [278].”