This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the Ecocyc Database
We have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database.
The EcoCyc Database
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coliK-12 MG1655.
Groups: Knowledge Spreadsheets for Symbolic Biocomputing
‘Groups’ is an implementation of Knowledge Spreadsheets (KSs) within the Pathway Tools system.
Data Mining in the Metacyc Family of Pathway Databases
The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB).
Groups: knowledge spreadsheets for symbolic biocomputing
Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database.
Regulatory Network Operations in the Pathway Tools Software
Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism’s genome and metabolic network.
Browsing Metabolic and Regulatory Networks with BioCyc
The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms.
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).