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Querying and computing with BioCyc databases

M. Krummenacker, S. Paley, L. Mueller, T. Yan, P. D. Karp
2005 Bioinformatics  
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

F. L. Fevre, S. Smidtas, V. Schachter
2007 Bioinformatics  
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

B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. M. Ozsoyoglu
2009 Bioinformatics  
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

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  
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

P. D. Karp
2005 Nucleic Acids Research  
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

Jesse R Walsh, Taner Z Sen, Julie A Dickerson
2014 BMC Systems Biology  
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

I. M. Keseler
2004 Nucleic Acids Research  
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]

Peter D. Karp, Natalia Ivanova, Markus Krummenacker, Nikos Kyrpides, Mario Latendresse, Peter Midford, Wai Kit Ong, Suzanne Paley, Rekha Seshadri
2018 arXiv   pre-print
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

B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. Meral Ozsoyoglu
2008 Bioinformatics  
: 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

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  
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

Peter Karp, Richard Billington, Timothy Holland, Anamika Kothari, Markus Krummenacker, Daniel Weaver, Mario Latendresse, Suzanne Paley
2015 Metabolites  
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

Peter D. Karp, Natalia Ivanova, Markus Krummenacker, Nikos Kyrpides, Mario Latendresse, Peter Midford, Wai Kit Ong, Suzanne Paley, Rekha Seshadri
2019 Frontiers in Microbiology  
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

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

Hierarchical Biological Pathway Data Integration and Mining [chapter]

Shubhalaxmi Kher, Jianling Peng, Eve Syrkin, Julie Dickerso
2012 Bioinformatics  
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

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.  ...  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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