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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi, Richard Billington, Luciana Ferrer, Hartmut Foerster, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Quang Ong, Suzanne Paley (+3 others)
2015 Nucleic Acids Research  
BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes  ...  The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.  ...  ACKNOWLEDGEMENT The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.  ... 
doi:10.1093/nar/gkv1164 pmid:26527732 pmcid:PMC4702838 fatcat:4i5okix5l5eyvdsfnccdzxqlym

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holland, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse (+8 others)
2013 Nucleic Acids Research  
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life.  ...  BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites,  ...  ACKNOWLEDGEMENTS The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the preceding agencies.  ... 
doi:10.1093/nar/gkt1103 pmid:24225315 pmcid:PMC3964957 fatcat:mfa4okdnxvhwrgf27kguvrss2q

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

R. Caspi, T. Altman, K. Dreher, C. A. Fulcher, P. Subhraveti, I. M. Keseler, A. Kothari, M. Krummenacker, M. Latendresse, L. A. Mueller, Q. Ong, S. Paley (+6 others)
2011 Nucleic Acids Research  
The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life.  ...  MetaCyc contains more than 1800 pathways derived from more than 30 000 publications, and is the largest curated collection of metabolic pathways currently available.  ...  The views and opinions of authors expressed herein do not necessarily state or reflect those of the US Government or any agency thereof.  ... 
doi:10.1093/nar/gkr1014 pmid:22102576 pmcid:PMC3245006 fatcat:zclxsx4caze4zc3sg7zsjxhhau

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller (+6 others)
2009 Nucleic Acids Research  
BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism.  ...  The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life.  ...  ACKNOWLEDGEMENTS We thank Dr Carol Bult and Dr Alexei Evsikov from the Jackson Laboratory for their contribution of pathways from the MouseCyc database.  ... 
doi:10.1093/nar/gkp875 pmid:19850718 pmcid:PMC2808959 fatcat:3mdlecp47rbszcro7wmgktztqi

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

R. Caspi, H. Foerster, C. A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S. Y. Rhee, A. G. Shearer, C. Tissier, T. C. Walk, P. Zhang (+1 others)
2007 Nucleic Acids Research  
BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/ Genome Databases (PGDBs).  ...  MetaCyc (MetaCyc.org) is a universal database of metabolic pathways and enzymes from all domains of life.  ...  We thank Adam Qwan for contributions to the chemical compound data and help with quality assurance of Pathway Tools.  ... 
doi:10.1093/nar/gkm900 pmid:17965431 pmcid:PMC2238876 fatcat:dz3ilfbpwbhdljbqnqvpezmoma

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

P. D. Karp
2005 Nucleic Acids Research  
Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from  ...  The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date.  ...  ACKNOWLEDGEMENTS This work was supported by grant GM70065 from the National Institutes of Health, by SRI International, and by EMBL-EBI.  ... 
doi:10.1093/nar/gki892 pmid:16246909 pmcid:PMC1266070 fatcat:ttfs5gffgvgebfj5fvozjybg2m

Cyclone: java-based querying and computing with Pathway/Genome databases

F. L. Fevre, S. Smidtas, V. Schachter
2007 Bioinformatics  
Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data.  ...  This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB.  ...  ACKNOWLEDGEMENTS We are grateful to the NeMo group for beta testing, to A. Yartseva for the 'Cyclone' name and to the P.Karp group at SRI, for its help with BioCyc.  ... 
doi:10.1093/bioinformatics/btm107 pmid:17392333 fatcat:qm3z2w46rnf4leeum5f4ssqix4

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

Kishori M Konwar, Niels W Hanson, Antoine P Pagé, Steven J Hallam
2013 BMC Bioinformatics  
, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools.  ...  Results: Here we present MetaPathways, an open source pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways  ...  Acknowledgements This work was carried out under the auspices of Genome Canada, Genome British Columbia, the Natural Science and Engineering Research Council (NSERC) of Canada, the Canadian Foundation  ... 
doi:10.1186/1471-2105-14-202 pmid:23800136 pmcid:PMC3695837 fatcat:ccsuukbfa5abvaqipo42rf76vq

Using genome-context data to identify specific types of functional associations in pathway/genome databases

Michelle L. Green, Peter D. Karp
2007 Computer applications in the biosciences : CABIOS  
Algorithm 1 extends our previous algorithm for identifying missing enzymes in predicted metabolic pathways (pathway holes) to use genome-context features.  ...  This algorithm performs with varying degrees of accuracy on each type of relationship, and performs best in predicting pathway and protein complex relationships.  ...  ACKNOWLEDGEMENTS We would like to thank the referees for their careful review of the manuscript and thoughtful suggestions for improvement. This work was supported in part by grant No.  ... 
doi:10.1093/bioinformatics/btm213 pmid:17646298 fatcat:7or7put53jdcxbnzat6wyicefu

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases

P. R. Romero, P. D. Karp
2004 Bioinformatics  
Pathway-genome databases (PGDBs) add metabolic and other organizational (i.e. protein complexes) information to the annotated genome, and are able to capture TU organization information.  ...  The augmented predictor has been implemented as part of our Pathway Tools software suite, and can be used to populate a PGDB with predicted TUs.  ...  This work was supported by DARPA contract N66001-01-C-8011, by NIH grant R01-HG02729-01, and by Department of Energy grant DE-FG03-01ER63219.  ... 
doi:10.1093/bioinformatics/btg471 pmid:14751985 fatcat:osapibjcjvf3hmhdmvc6bzyvje

Pathway Tools version 24.0: Integrated Software for Pathway/Genome Informatics and Systems Biology [article]

Peter D. Karp, Suzanne M. Paley, Peter E. Midford, Markus Krummenacker, Richard Billington, Anamika Kothari, Wai Kit Ong, Pallavi Subhraveti, Ingrid M. Keseler, Ron Caspi
2020 arXiv   pre-print
The software creates and manages a type of organism-specific database called a Pathway/Genome Database (PGDB), which the software enables database curators to interactively edit.  ...  Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions.  ...  Christos Ouzounis was a co-developer of the original metabolic pathway prediction algorithm, contributed an early version of the import/export system, and has been a source of much sound advice.  ... 
arXiv:1510.03964v4 fatcat:3plt5gcqmvg33pi6vd2mhufsda

The MetaCyc database of metabolic pathways and enzymes

Ron Caspi, Richard Billington, Carol A Fulcher, Ingrid M Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Quang Ong, Wai Kit Ong, Suzanne Paley, Pallavi Subhraveti (+1 others)
2017 Nucleic Acids Research  
MetaCyc (https://MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life.  ...  Meta-Cyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in the Bio-Cyc (https://BioCyc.org) and other PGDB collections  ...  ACKNOWLEDGEMENTS The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.  ... 
doi:10.1093/nar/gkx935 pmid:29059334 pmcid:PMC5753197 fatcat:fqyizu3bhrdhhdhcx2tslmdj6e

MetaCyc: a multiorganism database of metabolic pathways and enzymes

C. J. Krieger
2004 Nucleic Acids Research  
The MetaCyc database (see URL http://MetaCyc.org) is a collection of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants.  ...  MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to create Pathway/Genome Databases that can be augmented with curation  ...  ACKNOWLEDGEMENTS We are grateful to John Ingraham for his contributions to reviewing MetaCyc pathways and for his assistance in developing the MetaCyc pathway taxonomy.  ... 
doi:10.1093/nar/gkh100 pmid:14681452 pmcid:PMC308834 fatcat:lqw4rgxws5auzestjlw56xi36m

MetaCyc: a multiorganism database of metabolic pathways and enzymes

R. Caspi
2006 Nucleic Acids Research  
MetaCyc is a database of metabolic pathways and enzymes located at http://MetaCyc.org/.  ...  MetaCyc contains metabolic pathways, 20 enzymatic reactions, enzymes, chemical compounds, genes and review-level comments.  ...  Hong and Rama Balakrishnan for the Saccharomyces pathways they 80 submitted to MetaCyc, and Tanya Berardini, Leonore Reiser and Wolf Frommer for reviewing the cellular component ontology.  ... 
doi:10.1093/nar/gkj128 pmid:16381923 pmcid:PMC1347490 fatcat:bkg4ej4xxbcxfahisv3rnt3k2y

The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

2019 Database: The Journal of Biological Databases and Curation  
For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated  ...  The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways.  ...  The authors thank Cédric Cabau and Philippe Bardou for their help with the website. The authors are grateful to Gail Wagman for her correction of the English-language version.  ... 
doi:10.1093/database/baz049 pmid:31032842 pmcid:PMC6487390 fatcat:xt5futbmqzb5ti24egyouuviii
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