National Center for Biotechnology Information (NCBI) Organismal Classification

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The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.

Form

Core information

URL(s):

https://www.ncbi.nlm.nih.gov/

Publisher(s) / Maintainer(s):

National Center for Biotechnology Information (NCBI)

Domain(s):

Organisms, [Peripheral / neighbouring domains]

Type of standard:

Ontology

Additional information

Acronym:

NCBITAXON

Contact email:

info@ncbi.nlm.nih.gov

Technical information

Format of the data standard:

CSV, Turtle, UMLS (RRF, ORF)

Download / dump:

http://data.agroportal.lirmm.fr/ontologies/NCBITAXON/submissions/1/download?apik...

Link to machine-readable description:

https://data.bioontology.org/ontologies/NCBITAXON/download?apikey=4a5011ea-75fa-...

Relations

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

Cell Ontology, Country and Location , BioTop Ontology, Environment Ontology, Experimental Factor Ontology, French Crop Usage, Gramene Taxonomy Ontology, OntoBiotope, Plant Environment Ontology, Plant Ontology, Plant Trait Ontology, Population and Community Ontology, Protein Ontology, Semantic Types Ontology, Semanticscience Integrated Ontology, Thesaurus for Animal Physiology and Livestock Systems, Wheat Trait Ontology

VEST / AgroPortal integration

Original source:

AgroPortal

Agroportal URI:

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

Agroportal Web page:

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

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 specialized vocabulary management platform

Documented:

Yes

Supported:

Yes

Testable:

Yes

Machine-readable:

Yes

Meaningful:

Yes

Annotated:

Referenceable:

Yes

Linked:

Yes

Clearly licensed:

Yes

Openly licensed:

Yes

Scores

Avg usability:

3.29

Avg openness:

2.57

Notes on assessment:

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

URI: https://vest.agrisemantics.org/node/17603

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