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Querying and computing with BioCyc databases
2005
Bioinformatics
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We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program ...
Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. ...
ACKNOWLEDGEMENTS We thank Jeremy Zucker for the SBML exporter and Thomas J. Lee for his SQL example. ...
doi:10.1093/bioinformatics/bti546
pmid:15961440
pmcid:PMC1450015
fatcat:o5c3mpsy6nbovhl73nkryuwh5e
Cyclone: java-based querying and computing with Pathway/Genome databases
2007
Bioinformatics
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Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). ...
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. ...
Yartseva for the 'Cyclone' name and to the P.Karp group at SRI, for its help with BioCyc. This work was supported by BioSapiens, an EU FP6 Network of Excellence (contract number LSHG-CT-2003-503265). ...
doi:10.1093/bioinformatics/btm107
pmid:17392333
fatcat:qm3z2w46rnf4leeum5f4ssqix4
Corrigendum for Elliott,B. et al., 'PathCase pathways database system', Bioinformatics, Nov. 2008, 24(21), pp. 2526-2533
2009
Bioinformatics
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In the desktop version of BioCyc software, pathway drawings are also computed at query time. (2) Page 7, column 1, line 3: 'It is also possible to export visualizations of these databases to external applications ...
Here is a more detailed description of what happens with BioCyc. ...
doi:10.1093/bioinformatics/btp520
pmid:19713414
fatcat:zcqt54fjf5fqllhnytbj2kdwbi
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
2007
Nucleic Acids Research
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The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context. ...
BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/ Genome Databases (PGDBs). ...
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
2005
Nucleic Acids Research
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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 ...
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
A computational platform to maintain and migrate manual functional annotations for BioCyc databases
2014
BMC Systems Biology
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BioCyc databases are an important resource for information on biological pathways and genomic data. ...
Abstract Background: BioCyc databases are an important resource for information on biological pathways and genomic data. ...
Acknowledgements We thank the MaizeGDB team for sharing their insights and expertise. The MaizeGDB group also created a use case for this software and provided user feedback. ...
doi:10.1186/s12918-014-0115-1
pmid:25304126
pmcid:PMC4203924
fatcat:vc3quvywa5bytfyyznyeu7rmgy
EcoCyc: a comprehensive database resource for Escherichia coli
2004
Nucleic Acids Research
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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 ...
The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. ...
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
A Comparison of Microbial Genome Web Portals
[article]
2018
arXiv
pre-print
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We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. ...
The strengths of BioCyc include its genomic and metabolic tools, multi-search capabilities, table-based analysis tools, regulatory network tools and data, omics data analysis tools, breadth of data content ...
We thank Maulik Shukla of Argonne National Laboratory and the Univer- ...
arXiv:1810.12860v1
fatcat:tstzcyv7unhyblaqe74fpcp67u
PathCase: pathways database system
2008
Bioinformatics
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: an advanced querying interface for computer savvy users, and built-in queries for ease of use, that can be issued directly from pathway visualizations and (iv) a pathway functionality analysis tool. ...
The new features include: (i) a web-based system with a new architecture, containing a server-side and a client-side, and promoting scalability, and flexible and easy adaptation of different pathway databases ...
Querying: In addition to simple query forms that allow users to search for a keyword in database, BioCyc and Reactome provide advanced query interfaces that can add multiple predicates defined on different ...
doi:10.1093/bioinformatics/btn459
pmid:18728044
fatcat:25jn4wwelzahlp235bygmz2hha
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
2015
Nucleic Acids Research
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The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. ...
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 ...
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
Computational Metabolomics Operations at BioCyc.org
2015
Metabolites
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Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation ...
The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a "universal" metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. ...
The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. ...
doi:10.3390/metabo5020291
pmid:26011592
pmcid:PMC4495374
fatcat:e472ufnu35benczlo24p2v22ny
A Comparison of Microbial Genome Web Portals
2019
Frontiers in Microbiology
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We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. ...
The strengths of BioCyc include its genomic and metabolic tools, multi-search capabilities, table-based analysis tools, regulatory network tools and data, omics data analysis tools, breadth of data content ...
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
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
2009
Nucleic Acids Research
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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
Hierarchical Biological Pathway Data Integration and Mining
[chapter]
2012
Bioinformatics
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At present, the bioinformatics database owner only develops private system to provide user with data query and analysis services; such as NCBI develops Entrez database query system which is used on GenBank ...
The EVs to find a match for IEP and ND from GO in EV set above with those in BioCyc result in more than one likely match {GO: IEP → BioCyc: EV1, BioCyc: EV2}. ...
doi:10.5772/49974
fatcat:wo3ris5q5vfdjjdloan7phhche
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
2011
Nucleic Acids Research
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The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. ...
Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. ...
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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