PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.

Prefix

pato

Preferred Prefix

PATO

Version

2022-02-20

Links

Homepage Repository OBO OWL OBO JSON

Contact

George Gkoutos   0000-0002-2061-091X   gkoutos

Pattern for Local Unique Identifiers

Local identifiers in Phenotype And Trait Ontology should match this regular expression:
^\d{7}$

Example Local Unique Identifier

0001998   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Phenotype And Trait Ontology should match this regular expression:
^PATO:\d{7}$

Example CURIE

PATO:0001998

MIRIAM Namespace Embedded in LUI

The legacy MIRIAM standard for generating CURIEs with this resource includes the namespaceEmbeddedInLUI as true. The actual part that gets prefixed before the local unique identifier regex, otherwise known as the banana, is PATO:. Therefore, you might see local unique identifiers written out as CURIEs.

References

• Publication The anatomy of phenotype ontologies: principles, properties and applications
• Publication Using ontologies to describe mouse phenotypes

Appears In

AGRO AISM CDNO CL COLAO ECOCORE ECTO FOVT LEPAO MCO MS PCL PCO PHIPO PLANP RBO XPO ZP

The metaregistry provides mappings between the Bioregistry and other registries. There are 9 mappings to external registries for pato.

Providers are various services that resolve CURIEs to URLs. The example CURIE pato:0001998 is used to demonstrate the provides available for pato. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.