Registry EcoCyc

EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.

Prefix: ecocyc
Keywords: biopax genome/gene interaction/pathway metabolite protein rna sbml sequence
Links: Homepage
Publications: 2025 The EcoCyc database (2025); 2021 The EcoCyc Database in 2021; 2016 The EcoCyc database: reflecting new knowledge about Escherichia coli K-12; 2014 The EcoCyc Database; 2012 EcoCyc: fusing model organism databases with systems biology; https://bioregistry.io/pubmed:21097882

Identifier Standards

Pattern for Local Unique Identifiers: Missing LUI pattern
Example Local Unique Identifier: AICARTRANSIMPCYCLO-CPLX Resolve
Example CURIE: ecocyc:AICARTRANSIMPCYCLO-CPLX

Contacts

Contact: Peter D. Karp 0000-0002-5876-6418 pkarp111
Contributors: contributor Chris Mungall 0000-0002-6601-2165 cmungall

Ontology

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

In Collection (1): Global Biodata Coalition - Global Core Biodata Resources

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 5 mappings to external registries with 4 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
GO	`go`	`EcoCyc`
Integbio	`integbio`	`nbdc00262`
NCBI	`ncbi`	`ECOCYC`
Pathguide	`pathguide`	`9`
re3data	`re3data`	`r3d100011277`

Providers

Suggest

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 AICARTRANSIMPCYCLO-CPLX is used to demonstrate the providers available for EcoCyc. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Provider Name	Provider Code	URI
EcoCyc	`ecocyc`	https://ecocyc.org/gene?id=AICARTRANSIMPCYCLO-CPLX
Bioregistry	`bioregistry`	https://bioregistry.io/ecocyc:AICARTRANSIMPCYCLO-CPLX

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("ecocyc")
'EcoCyc'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("ecocyc")
'https://ecocyc.org/'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("ecocyc")
'Peter D. Karp'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("ecocyc")
'pkarp@ai.sri.com'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("ecocyc")
'pkarp111'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("ecocyc")
'0000-0002-5876-6418'