MIRA Epi Metaregistry - Experimental Factor Ontology

Registry Experimental Factor Ontology

The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.

Prefix: efo
Preferred Prefix: EFO
Version: 3.48.0
Links: Homepage Repository OBO OWL
Contact: Trish Whetzel 0000-0002-3458-4839 twhetzel
Pattern for Local Unique Identifiers: Local identifiers in Experimental Factor Ontology should match this regular expression:
^\d{7}$
Example Local Unique Identifier: 0005147 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Experimental Factor Ontology should match this regular expression:
^efo:\d{7}$
Example CURIE: efo:0005147
Publications: 2010 Modeling sample variables with an Experimental Factor Ontology.

Metaregistry Experimental Factor Ontology

The metaregistry provides mappings between the Bioregistry and other registries. There are 11 mappings to external registries for efo with 2 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
AberOWL	`aberowl`	`EFO`
AgroPortal	`agroportal`	`EFO`
BioContext	`biocontext`	`EFO`
Biolink Model Registry	`biolink`	`EFO`
BioPortal Prefixes	`bioportal`	`EFO`
Cellosaurus Registry	`cellosaurus`	`EFO`
FAIRSharing	`fairsharing`	`FAIRsharing.1gr4tz`
Identifiers.org	`miriam`	`efo`
Name-to-Thing	`n2t`	`efo`
Ontology Lookup Service	`ols`	`efo`
OntoBee	`ontobee`	`EFO`

Providers

Providers are various services that resolve CURIEs to URLs. The example CURIE efo:0005147 is used to demonstrate the provides available for efo. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.

Name	Metaprefix	URI
Experimental Factor Ontology	`efo`	http://www.ebi.ac.uk/efo/EFO_0005147
Bioregistry	`bioregistry`	https://bioregistry.io/efo:0005147
Identifiers.org	`miriam`	https://identifiers.org/efo:0005147
Name-to-Thing	`n2t`	https://n2t.net/efo:0005147
None	`ebi`	https://www.ebi.ac.uk/efo/EFO_0005147

Extra Providers

Additional providers curated in the Bioregistry are listed here.

Code	Name	URL
`ebi`	EFO through Functional Genomics Group (EBI)	https://www.ebi.ac.uk/efo/EFO_0005147

Get the version:

>>> import bioregistry as br
>>> br.get_version("efo")
'3.48.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("efo")
'http://www.ebi.ac.uk/efo'

Get the repository:

>>> import bioregistry as br
>>> br.get_repository("efo")
'https://github.com/EBISPOT/efo/'

Get the OBO download link:

>>> import bioregistry as br
>>> br.get_obo_download("efo")
'http://www.ebi.ac.uk/efo/efo.obo'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("efo")
'http://www.ebi.ac.uk/efo/efo.owl'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("efo")
'Trish Whetzel'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("efo")
'plwhetzel@gmail.com'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("efo")
'twhetzel'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("efo")
'0000-0002-3458-4839'