Cell Ontology | Agrisemantics Map of Data Standards

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The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This ontology is not organism specific it covers cell types from prokaryotes to mammals. However, it excludes plant cell types, which are covered by PO. See the website http://cellontology.org for more details.

Form

Core information

URL(s):

https://github.com/obophenotype/cell-ontology

Publisher(s) / Maintainer(s):

OBO Technical WG

Domain(s):

Animal Science and Animal Products

Type of standard:

Ontology

Describes / models / annotates:

Livestock research data, Research and agronomic data

Additional information

Acronym:

Other contributor(s):

Chris Mungall

Nicole Vasilevsky

Melissa Haendel

Alan Ruttenberg

Jane Lomax

David Osumi-Sutherland

Contact email:

addiehl@buffalo.edu

License(s):

Creative Commons Attribution

Technical information

Format of the data standard:

CSV, OBO Flat File, RDF/XML

Namespace:

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

Download / dump:

http://data.agroportal.lirmm.fr/ontologies/CL/submissions/5/download?apikey=1de0...

Link to machine-readable description:

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

Relations

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

Environment Ontology, Experimental Factor Ontology, Gene Ontology, National Center for Biotechnology Information (NCBI) Organismal Classification, OntoBiotope, Plant Trait Ontology, Protein Ontology, BioTop Ontology, GENO Ontology, Phenotypic Quality Ontology, Thesaurus for Animal Physiology and Livestock Systems

RDF vocabulary

Number of classes:

6546

Number of properties:

VEST / AgroPortal integration

Original source:

AgroPortal

Agroportal URI:

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

Agroportal Web page:

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

Assessment

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

Total score:

2.46

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 a collaborative environment (e.g. Github)

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:

2.86

Avg openness:

3.00

Notes on assessment:

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

URI: https://vest.agrisemantics.org/node/17585

RDF

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