Phenotypic Quality Ontology | Agrisemantics Map of Data Standards

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Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.

Form

Core information

URL(s):

https://github.com/pato-ontology

Publisher(s) / Maintainer(s):

OBO Technical WG

Domain(s):

Plant Science and Plant Products

Type of standard:

Ontology

Describes / models / annotates:

Phenotype and Trait, Biodiversity and ecological data, Plants / germplasm, Research and agronomic data, Natural Resources, Earth and Environment data

Additional information

Acronym:

PATO

Contact email:

geg18@aber.ac.uk

License(s):

Creative Commons Attribution

Technical information

Format of the data standard:

CSV, OBO Flat File, RDF/XML

Namespace:

http://purl.obolibrary.org/obo/pato.owl

Download / dump:

http://data.agroportal.lirmm.fr/ontologies/PATO/submissions/4/download?apikey=1d...

Link to machine-readable description:

http://purl.obolibrary.org/obo/pato.owl

Relations

Aligned / mapped to (link to vocabulary in the map):

Environment Ontology, Experimental Factor Ontology, Gene Ontology, GENO Ontology, Lentil Ontology, Banana Ontology, Cell Ontology, Plant Trait Ontology, Population and Community Ontology, Semanticscience Integrated Ontology, Soybean Ontology, XEML Environment Ontology, Thesaurus for Animal Physiology and Livestock Systems

RDF vocabulary

RDF "language":

OBO

Number of classes:

2616

Number of properties:

VEST / AgroPortal integration

Original source:

AgroPortal

Agroportal URI:

http://data.agroportal.lirmm.fr/ontologies/PATO

Agroportal Web page:

http://agroportal.lirmm.fr/ontologies/PATO

Assessment

An overview of criteria used for the assessment can be found here.

Total score:

2.50

assessment tabs

Fitness / adoption

Complete:

Fairly complete but needs complementary vocabularies

Authoritative:

Not clear - N/A

Largely compatible:

Yes

Known:

Yes, moderately

Used in software:

Yes, in a few tools

Used in datasets:

Not clear - N/A

Discoverable:

Yes

Regulatory:

Not clear - N/A

Endorsed:

Yes, moderately

Long-term, sustainable:

Not clear - N/A

Participatory, collaborative:

Not clear - N/A

Maintained:

Not clear - N/A

Scores

Avg fitness:

2.33

Avg adoption:

1.67

Usability / openness

Available on the web:

Yes

Versatile:

Yes, 2-3 similar formats

Served by APIs:

Yes, to get web- or user- friendly results

Yes, to lookup terms / concepts using several parameters

Yes, to automatically annotate text or data

Yes, to perform cross-walks between vocabularies

Manageable:

Yes, on specialized vocabulary management platform

Documented:

Yes

Supported:

Yes

Testable:

Not clear - N/A

Machine-readable:

Yes

Meaningful:

Yes

Annotated:

Yes

Referenceable:

Yes

Linked:

Yes

Clearly licensed:

Yes

Openly licensed:

Yes

Scores

Avg usability:

3.00

Avg openness:

3.00

Notes on assessment:

First technical assessment (usability / openness) made by: Agroknow.

URI: https://vest.agrisemantics.org/node/17615

RDF

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