Querying and Computing with BioCyc Databases


Krummenacker, M., Paley, S., Mueller, L., Yan, T., and Karp, P.D. Querying and Computing with BioCyc Databases. Bioinformatics, vol. 21, pp. 3454-5, 2005.



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.


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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