BioCyc Database Collection

BioCyc is a collection of 14735 Pathway/Genome Databases (PGDBs), plus software tools for exploring them [Karp17]. Key aspects of BioCyc data:

• Quality data curated from tens of thousands of publications, including curated databases for E. coli, B. subtilis, H. sapiens, and S. cerevisiae.
• Computationally predicted metabolic pathways and operons.
• Data integrated from other databases including gene essentiality, regulatory networks, protein features, and GO annotations.

Current version: 23.1, released on Sept 19, 2019. Update History

Subscriptions are required to access most of BioCyc beyond a limited period of free use. For more information on obtaining a subscription, click here. Subscriptions support curation of BioCyc content on a non-profit basis. You do not need a subscription to access EcoCyc or MetaCyc, or if your institution already subscribes (institution name is in the top right corner of this page, or appears here.)

New to BioCyc? Typical usage is:

• Select a database (genome) to search by clicking "change organism database" in the box in the top right of every page.
• Search for a gene, pathway, metabolite, or enzyme using the Quick Search in that same box, or see the Search menu for more options.

BioCyc Tools

BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:

• Genome browser
• Display of individual metabolic pathways, and of full metabolic maps
• Multiple omics data analysis methods for user-supplied omics and multi-omics datasets including the Omics Dashboard, painting onto pathway diagrams and metabolic maps, and tables of perturbed pathways
• Store groups of genes, metabolites, etc. in your account as SmartTables; share, analyze, transform those groups
• Metabolic route search tools
• Run metabolic models
• Comparative analysis tools

BioCyc Databases

The BioCyc databases are divided into three tiers, based on their quality.

Tier 1 databases have received at least one person-year of literature-based curation, and are the most accurate. EcoCyc and MetaCyc have each received more than 20 person-years of curation.

Tier 2 and Tier 3 databases contain computationally predicted metabolic pathways, predictions as to which genes code for missing enzymes in metabolic pathways, and predicted operons.

Funding Sources

The development of BioCyc is funded by NIH grants GM080746, GM077678, and GM075742 from the NIH National Institute of General Medical Sciences, and by BioCyc subscription revenues.