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
Metaregistry Phenotype And Trait Ontology

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.

Registry Name Registry Metaprefix External Prefix Curate
AberOWL AberOWL logo aberowl PATO
AgroPortal AgroPortal logo agroportal PATO
BioContext biocontext PATO
BioPortal BioPortal Prefixes logo bioportal PATO
FAIRSharing FAIRSharing logo fairsharing FAIRsharing.ezwdhz
GO Gene Ontology Registry logo go PATO
Identifiers.org Identifiers.org logo miriam pato
N2T Name-to-Thing logo n2t pato
OBO Foundry OBO Foundry logo obofoundry pato
OLS Ontology Lookup Service logo ols pato
OntoBee OntoBee logo ontobee PATO
Prefix Commons Prefix Commons logo prefixcommons pato
RDF Information

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

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

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 0001998 is used to demonstrate the providers available for Phenotype And Trait Ontology. A guide for curating additional providers can be found here.

Name Metaprefix URI
Phenotype And Trait Ontology pato http://purl.obolibrary.org/obo/PATO_0001998
Phenotype And Trait Ontology (RDF) rdf http://purl.obolibrary.org/obo/PATO_0001998
Bioregistry bioregistry https://bioregistry.io/pato:0001998
Identifiers.org miriam https://identifiers.org/PATO:0001998
OBO Foundry obofoundry http://purl.obolibrary.org/obo/PATO_0001998
Ontology Lookup Service ols https://www.ebi.ac.uk/ols4/ontologies/pato/terms?iri=http://purl.obolibrary.org/obo/PATO_0001998
Name-to-Thing n2t https://n2t.net/pato:0001998
BioPortal Prefixes bioportal https://bioportal.bioontology.org/ontologies/PATO/?p=classes&conceptid=http://purl.obolibrary.org/obo/PATO_0001998
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/pato:0001998
purl Legacy PURL http://purl.org/obo/owl/PATO#PATO_0001998