BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.

Prefix

biocyc

Keywords

genome pathway sequence

Links

Homepage

Contact

Peter D. Karp   0000-0002-5876-6418   pkarp111

Pattern for Local Unique Identifiers

Local identifiers in BioCyc collection of metabolic pathway databases should match this regular expression:
^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$

Example Local Unique Identifier

ECOLI:CYT-D-UBIOX-CPLX   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from BioCyc collection of metabolic pathway databases should match this regular expression:
^biocyc:[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$

Example CURIE

biocyc:ECOLI:CYT-D-UBIOX-CPLX

Publications

• https://bioregistry.io/pubmed:29447345
• 2015 The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
• 2005 Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

The metaregistry provides mappings between the Bioregistry and other registries. There are 9 mappings to external registries for this resource with 5 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier ECOLI:CYT-D-UBIOX-CPLX is used to demonstrate the providers available for BioCyc collection of metabolic pathway databases. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.