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Bioinformatics Advance Access published online on June 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti546
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 12, 2005
Revised June 14, 2005
Accepted June 14, 2005

Applications note

Querying and computing with BioCyc databases

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

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

* To whom correspondence should be addressed.
Peter D. Karp, E-mail: pkarp{at}ai.sri.com


  Abstract

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.


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