Querying and computing with BioCyc databases

Authors:
Markus Krummenacker;Suzanne Paley;Lukas Mueller;Thomas Yan;Peter D. Karp
Affiliations:
SRI International, Bioinformatics Research Group EK207 Menlo Park, CA 94025, USA;SRI International, Bioinformatics Research Group EK207 Menlo Park, CA 94025, USA;Cornell University, Department of Plant Breeding and Genetics Emerson Hall Ithaca, NY 14853, USA;Carnegie Institution of Washington, Department of Plant Biology Stanford, CA 94305, USA;SRI International, Bioinformatics Research Group EK207 Menlo Park, CA 94025, USA
Venue:
Bioinformatics
Year:
2005

Citing 0
Cited 4

Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics

Reasoning Web
Advanced querying interface for biochemical network databases

Proceedings of the 2010 ACM Symposium on Applied Computing
Modeling without borders: creating and annotating VCell models using the web

ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Domain specific vs generic network visualization: an evaluation with metabolic networks

AUIC '11 Proceedings of the Twelfth Australasian User Interface Conference - Volume 117

Quantified Score

Hi-index	3.84

Visualization

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 Contact: pkarp@ai.sri.com