Registry BioCyc collection of metabolic pathway databases

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
Metaregistry BioCyc collection of metabolic pathway databases

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.

Registry Name Registry Metaprefix External Prefix Curate
BioContext biocontext BIOCYC
EDAM EDAM Ontology logo edam 2104
GO Gene Ontology Registry logo go BioCyc
Integbio Integbio logo integbio nbdc00252
Identifiers.org Identifiers.org logo miriam biocyc
N2T Name-to-Thing logo n2t biocyc
Pathguide Pathguide logo pathguide 8
Prefix Commons Prefix Commons logo prefixcommons biocyc
UniProt UniProt Cross-ref database logo uniprot DB-0005
Providers

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.

Name Metaprefix URI
BioCyc collection of metabolic pathway databases biocyc http://biocyc.org/getid?id=ECOLI:CYT-D-UBIOX-CPLX
Bioregistry bioregistry https://bioregistry.io/biocyc:ECOLI:CYT-D-UBIOX-CPLX
Identifiers.org miriam https://identifiers.org/biocyc:ECOLI:CYT-D-UBIOX-CPLX
Name-to-Thing n2t https://n2t.net/biocyc:ECOLI:CYT-D-UBIOX-CPLX
Extra Providers

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

Code Name URL
bio2rdf Bio2RDF http://bio2rdf.org/biocyc:ECOLI:CYT-D-UBIOX-CPLX