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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 collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of  ...  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

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).  ...  The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.  ...  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

A Comparison of Microbial Genome Web Portals [article]

Peter D. Karp, Natalia Ivanova, Markus Krummenacker, Nikos Kyrpides, Mario Latendresse, Peter Midford, Wai Kit Ong, Suzanne Paley, Rekha Seshadri
2018 arXiv   pre-print
The strengths of KEGG include its genomic and metabolic tools. The strengths of Ensembl Bacteria include its genomic tools and large number of genomes.  ...  The strengths of KBase include its genomic tools and metabolic models.  ...  We thank Maulik Shukla of Argonne National Laboratory and the Univer-  ... 
arXiv:1810.12860v1 fatcat:tstzcyv7unhyblaqe74fpcp67u

A Comparison of Microbial Genome Web Portals

Peter D. Karp, Natalia Ivanova, Markus Krummenacker, Nikos Kyrpides, Mario Latendresse, Peter Midford, Wai Kit Ong, Suzanne Paley, Rekha Seshadri
2019 Frontiers in Microbiology  
The strengths of KEGG include its genomic and metabolic tools. The strengths of Ensembl Bacteria include its genomic tools and large number of genomes.  ...  The strengths of KBase include its genomic tools and metabolic models.  ...  We thank Maulik Shukla of Argonne National Laboratory and the University of Chicago and Rebecca Wattam of Virginia Tech for comments and corrections regarding PATRIC.  ... 
doi:10.3389/fmicb.2019.00208 pmid:30853946 pmcid:PMC6395428 fatcat:lefxs2tduvdtpasalfebkozm7u

ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods

Patrice Baa-Puyoulet, Nicolas Parisot, Gérard Febvay, Jaime Huerta-Cepas, Augusto F. Vellozo, Toni Gabaldón, Federica Calevro, Hubert Charles, Stefano Colella
2016 Database: The Journal of Biological Databases and Curation  
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.  ...  In this context, we present here ArthropodaCyc, a dedicated BioCyc collection of databases using the Cyc annotation database system (CycADS), allowing researchers to perform reliable metabolism comparisons  ...  The authors would also like to thank the following resources for genome sequence data: AphidBase (http://www.aphidbase.com/) (52) Conflict of interest. None declared.  ... 
doi:10.1093/database/baw081 pmid:27242037 pmcid:PMC5630938 fatcat:dpq2cagvujb3hm2s7dg2xmjihe

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.  ...  With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available.  ...  We thank Dr Lindsay Eltis and Dr Hao-Ping Chen from the University of British Columbia for their contribution of pathways from the Rhodococcus jostii RHA1 database.  ... 
doi:10.1093/nar/gkp875 pmid:19850718 pmcid:PMC2808959 fatcat:3mdlecp47rbszcro7wmgktztqi

MetaCyc: a multiorganism database of metabolic pathways and enzymes

R. Caspi
2006 Nucleic Acids Research  
Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to 15 small molecule metabolism, which have been reported in the experimental literature.  ...  MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, edu-30 cation, metabolic engineering and systems biology.  ...  This work was supported by grant R01-85 RR07861-01 from the NIH National Institute of General Medical Sciences, and by grant R01-HG02729-01 from the NIH National Human Genome Research Institute.  ... 
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  
The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways.  ...  Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic 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

Integration of bioinformatics to biodegradation

Pankaj Arora, Hanhong Bae
2014 Biological Procedures Online  
(Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation.  ...  Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.  ...  This database was developed and curated by the BioCyc group at SRI international. BioCyc (http://biocyc.org/) is a collection of more than 2988 organism-specific Pathway/Genome Databases (PGDBs).  ... 
doi:10.1186/1480-9222-16-8 pmid:24808763 pmcid:PMC4012781 fatcat:y6m3tkkm5jafzmg643aoliriue

Metabolic route computation in organism communities

Markus Krummenacker, Mario Latendresse, Peter D Karp
2019 Microbiome  
The challenge we address is understanding the overall metabolic capabilities of a microbiome: through what series of metabolic transformations can a microbiome convert a starting compound to an ending  ...  Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes.  ...  Competing interests SRI receives royalties from licensing of the Pathway Tools software and from subscription fees from the BioCyc website.  ... 
doi:10.1186/s40168-019-0706-6 pmid:31174602 pmcid:PMC6556054 fatcat:khozk4mihrelnkrvxxcwrhrf3a

An In-Silico Approach of Polyhydroxybutyrate Synthesis and Phylogeny Study for Degradation of Polyhydroxybutyrate in Organisms from Lower to Higher Organization

Shivangi Shrivastava
2021 International Journal for Research in Applied Science and Engineering Technology  
The study covered the new ideas which can able to change the approach of biosynthesis of PHB in microorganisms and degradation of biopolymer without any harmful effect on environment as well as ecosystem  ...  There are much data is available on databases which helps to complete the future study related to medicine, environment and nano-technology.  ...  Metabolic pathways the utilisation of macromolecules for further reations. Metabolic pathway for polyhydroxybutyrate synthesis invivo was observed and studied with BioCyc.  ... 
doi:10.22214/ijraset.2021.38520 fatcat:rye7cz3mbnd6hkzndwtsnkuu4e

EcoCyc: a comprehensive database resource for Escherichia coli

I. M. Keseler
2004 Nucleic Acids Research  
binding sites, metabolic pathways, functionally related genes, protein complexes and protein-ligand interactions.  ...  The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying  ...  ACKNOWLEDGEMENTS We thank Martha Arnaud, Robert Gunsalus, Randy Gobbel, John Pick, C e esar Bonavides-Martinez and Alberto Santos-Zavaleta for their contributions to EcoCyc and to Pathway Tools.  ... 
doi:10.1093/nar/gki108 pmid:15608210 pmcid:PMC540062 fatcat:pryrhmotizgw5ndaofvwqw7coq

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

Valérie de Crécy-Lagard
2014 Computational and Structural Biotechnology Journal  
Comparing THF pathway reconstructions and functional annotations of a chosen set of folate synthesis genes in specific prokaryotes revealed the strengths and weaknesses of different microbial annotation  ...  The THF biosynthesis pathway and enzymes are, however, not universal and alternate solutions are found for most steps, making this pathway a challenge to annotate automatically in many genomes.  ...  Manual Annotation of Proteins (HAMAP); Integrated Microbial Genomes (IMG); PAThogen Resource Integration Center (PATRIC); Kyoto Encyclopedia of Genes and Genomes (KEGG); Comprehensive Microbial Resource  ... 
doi:10.1016/j.csbj.2014.05.008 pmid:25210598 pmcid:PMC4151868 fatcat:kqaw67neyvgifm3v7tcscmxb7e

Global genome analysis of the shikimic acid pathway reveals greater gene loss in host-associated than in free-living bacteria

Jurica Zucko, Walter C Dunlap, J Malcolm Shick, John Cullum, François Cercelet, Bijal Amin, Lena Hammen, Timothy Lau, Jamal Williams, Daslav Hranueli, Paul F Long
2010 BMC Genomics  
The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic pathways.  ...  The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes.  ...  ); a cooperation grant of the German Academic Exchange Service (DAAD) and the Ministry of Science, Education and Sports, Republic of Croatia (to DH and JC), by a stipendium of the DAAD (to JZ).  ... 
doi:10.1186/1471-2164-11-628 pmid:21070645 pmcid:PMC3018139 fatcat:ilmoufc5dbd37o775m47yi43aa

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  
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 MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life.  ...  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
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