BioCyc Knowledge Library

BioCyc Knowledge Library provides curated pathway/genome databases and computational resources for analysis of metabolic pathways, enzyme functions, and regulatory networks across organisms.

Key Features:

• Database collection: A collection of pathway/genome databases including MetaCyc, EcoCyc, HumanCyc, and other organism-specific databases.
• MetaCyc: A review-level metabolic-pathway database integrating literature-curated data that describes 445 pathways and 1,115 enzymes across 158 organisms with pathways determined experimentally and annotated with species provenance.
• EcoCyc: An organism-specific pathway/genome database for Escherichia coli providing detailed descriptions of metabolic and signal-transduction pathways, enzymes, transport proteins, and transcriptional control mechanisms.
• Integration of experimental data and literature citations: Pathways and enzymes are supported by experimental evidence and linked to literature references for species annotation.
• Pathway Tools software: Provides query operations and visualization capabilities for pathway and genome analysis.
• Data formats: Databases are available in flatfiles for local computational use.

Scientific Applications:

• Pathway analysis of genomes: Use MetaCyc data to analyze and interpret metabolic pathways encoded in genomes.
• Metabolic engineering: Support design and modification of metabolic pathways using curated pathway and enzyme information.
• Biochemistry education: Provide curated pathway and enzyme descriptions for teaching biochemical pathway organization and function.
• Genomics and systems biology research: Facilitate integrative analyses of metabolic networks and regulatory interactions across organisms.
• Escherichia coli network annotation: Enable annotation and analysis of E. coli metabolic and regulatory networks using EcoCyc.

Methodology:

MetaCyc integrates information from multiple literature sources and annotates experimentally determined pathways with species-level references; Pathway Tools provides query operations and visualization, and databases are distributed in flatfile format.