Skip Navigation


Bioinformatics Advance Access originally published online on June 16, 2005
Bioinformatics 2005 21(16):3454-3455; doi:10.1093/bioinformatics/bti546
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/16/3454    most recent
bti546v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (16)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Krummenacker, M.
Right arrow Articles by Karp, P. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Krummenacker, M.
Right arrow Articles by Karp, P. D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Querying and computing with BioCyc databases

Markus Krummenacker 1, Suzanne Paley 1, Lukas Mueller 2, Thomas Yan 3 and Peter D. Karp 1,*

1SRI International, Bioinformatics Research Group EK207 Menlo Park, CA 94025, USA
2Cornell University, Department of Plant Breeding and Genetics Emerson Hall Ithaca, NY 14853, USA
3Carnegie Institution of Washington, Department of Plant Biology Stanford, CA 94305, USA

*To whom correspondence should be addressed.

Summary: 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.

Availability: The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml

Supplementary information: For more details on programmatic access to BioCyc DBs, see http://bioinformatics.ai.sri.com/ptools/ptools-resources.html

Contact: pkarp{at}ai.sri.com

Received on April 12, 2005; revised on June 14, 2005; accepted on June 14, 2005

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
T. J. Lee, I. Paulsen, and P. Karp
Annotation-based inference of transporter function
Bioinformatics, July 1, 2008; 24(13): i259 - i267.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
P. N. Bertin, C. Medigue, and P. Normand
Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems
Microbiology, February 1, 2008; 154(2): 347 - 359.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. S. Wishart, D. Tzur, C. Knox, R. Eisner, A. C. Guo, N. Young, D. Cheng, K. Jewell, D. Arndt, S. Sawhney, et al.
HMDB: the Human Metabolome Database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D521 - D526.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Vallenet, L. Labarre, Z. Rouy, V. Barbe, S. Bocs, S. Cruveiller, A. Lajus, G. Pascal, C. Scarpelli, and C. Medigue
MaGe: a microbial genome annotation system supported by synteny results
Nucleic Acids Res., January 10, 2006; 34(1): 53 - 65.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, et al.
The UCSC Genome Browser Database: update 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D590 - D598.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Jaiswal, J. Ni, I. Yap, D. Ware, W. Spooner, K. Youens-Clark, L. Ren, C. Liang, W. Zhao, K. Ratnapu, et al.
Gramene: a bird's eye view of cereal genomes
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D717 - D723.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. D. Karp, C. A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahren, S. Tsoka, N. Darzentas, V. Kunin, and N. Lopez-Bigas
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Nucleic Acids Res., October 24, 2005; 33(19): 6083 - 6089.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.