Querying and Computing with BioCyc Databases

Citation

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.

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

↓ Review online

Read more from SRI

  • surgeons around a surgical robot

    The SRI research behind today’s surgical robotics

    Intuitive’s da Vinci 5 system represents a major leap in robotic-assisted medicine. It all started at SRI, which continues to advance teleoperation technologies.

  • a collage of digital graphs

    A banner year for quantum

    SRI-managed QED-C’s annual report on quantum trends captures an industry accelerating rapidly from technical promise toward major global impact.

  • ICE Cube containing SRI’s aerogel experiment, photographed prior to launch. Source: Aerospace Applications North America

    An SRI carbon capture experiment launches into space

    By synthesizing carbon-absorbing aerogels in microgravity, SRI research will give us a rare glimpse into how these materials could be radically improved.