GENO Ontology | Agrisemantics Map of Data Standards

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It is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxonomy, the revisions were made as and when/where required in the rankings. The rank of genome types was added by this project. This taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.

Form

Core information

URL(s):

https://github.com/monarch-initiative/GENO-ontology/

Type of standard:

Ontology

Describes / models / annotates:

Research and agronomic data, Plants / germplasm, General Germplasm, Phenotype and Trait, Plant Anatomy and Development

Additional information

Acronym:

GENO

Contact email:

brushm@ohsu.edu

Technical information

Format of the data standard:

CSV, OWL/XML, RDF/XML

Relations

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

BioTop Ontology, Environment Ontology, Cell Ontology, Experimental Factor Ontology, Genomic Feature and Variation Ontology, Phenotypic Quality Ontology, Population and Community Ontology, Process and Observation Ontology, Semanticscience Integrated Ontology, Sequence Types and Features Ontology, Single-Nucleotide Polymorphism (SNP) Ontology, Variation Ontology, Plant Trait Ontology

RDF vocabulary

RDF "language":

OWL

VEST / AgroPortal integration

Original source:

AgroPortal

Agroportal URI:

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

Agroportal Web page:

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

Assessment

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

Total score:

2.14

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:

Not clear - N/A

Supported:

Not clear - N/A

Testable:

Not clear - N/A

Machine-readable:

Yes

Meaningful:

Yes

Annotated:

Not clear - N/A

Referenceable:

Yes

Linked:

Yes

Clearly licensed:

Not clear - N/A

Openly licensed:

Not clear - N/A

Scores

Avg usability:

2.43

Avg openness:

2.14

Notes on assessment:

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

URI: https://vest.agrisemantics.org/node/17579

RDF

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