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

Keywords

biodiversity biology obo ontology phenotype quality

Version

2024-03-28

License

CC-BY-3.0

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 annotates the namespaceEmbeddedInLUI as true. This means that you may see local unique identifiers that include a redundant prefix and delimiter (also known as a banana) and therefore look like a CURIE. For Phenotype And Trait Ontology, the banana looks like PATO:. Therefore, you may see local unique identifiers for this resource that look like PATO:0001998 (instead of the canonical form 0001998) and CURIEs for this resource that look like PATO:PATO:0001998 (instead of the canonical form PATO:0001998). The Bioregistry will automatically strip off the banana when standardizing local unique identifiers and CURIEs.

Publications

• 2018 The anatomy of phenotype ontologies: principles, properties and applications
• 2010 Integrating phenotype ontologies across multiple species
• 2004 Using ontologies to describe mouse phenotypes

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

Appears In (21) (bioregistry.schema:0000018 )

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

The metaregistry provides mappings between the Bioregistry and other registries. There are 12 mappings to external registries for this resource with 2 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

http://purl.obolibrary.org/obo/PATO_$1

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 0001998 is used to demonstrate the providers available for Phenotype And Trait Ontology. 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.