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

bibliography/documents biopax dna enzyme and pathway databases genome genome/gene interaction/pathway pathway protein rna sbml sequence

Links

Homepage

Publications

2019 The BioCyc collection of microbial genomes and metabolic pathways

2015 The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

https://bioregistry.io/pubmed:22102576

2005 Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

Pattern for Local Unique Identifiers

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

Example CURIE

biocyc:ECOLI:CYT-D-UBIOX-CPLX

Contact

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

A summary of the relations in the Bioregistry schema can be found here.

In Collection (1)

Synapse.org external links

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 9 mappings to external registries 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. Some providers may use a different example, which is displayed in the table below. 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.