URI*
http://purl.bioontology.org/ontology/NCBITAXON/
http://purl.bioontology.org/ontology/NCBITAXON/
Abstract
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration (INSDC). It provides a framework for clustering elements within other domains of NCBI web pages, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web and relevant publications. It is also the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC) that comprises of GenBank, the European Molecular Biology Laboratory (EMBL) and DNA Data Bank of Japan (DDBJ). It consists of a curated set of names and classifications for all of the source organisms represented in the INSDC. The NCBI taxonomy database contains a list of names that are determined to be nomenclaturally correct or valid (as defined according to the different codes of nomenclature), classified in an approximately phylogenetic hierarchy (depending on the level of knowledge regarding phylogenetic relationships of a given group) as well as a number of names that exist outside the jurisdiction of the codes. That is, it focuses on nomenclature and systematics, rather than documenting the description of taxa. It requires a curator to select a current name out of all possible names for a specific taxon. This is done by a specialist at the NCBI Taxonomy database, relying on published taxonomic data and external expert opinion. This single, current name are indicated on all INSDC records. See more...
Bug database
https://github.com/obophenotype/ncbitaxon/issues
https://github.com/obophenotype/ncbitaxon/issues
Comes from the same domain
https://data.agroportal.lirmm.fr/ontologies/GR-TAX
https://data.agroportal.lirmm.fr/ontologies/GR-TAX
https://data.agroportal.lirmm.fr/ontologies/TAXREF-LD
https://data.agroportal.lirmm.fr/ontologies/TAXREF-LD
Contact*
Ncbi Information (info@ncbi.nlm.nih.gov)
Object creation date property
http://purl.org/dc/elements/1.1/created
http://purl.org/dc/elements/1.1/created
Submission date
August 27, 2023
Deprecated
false See more...
Description*
The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet. See more...
Documentation
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/
Example of resource
http://purl.bioontology.org/ontology/NCBITAXON/201174 See more...
Subject
https://data.agroportal.lirmm.fr/categories/TAX See more...
Formality level
http://w3id.org/nkos/nkostype#taxonomy
http://w3id.org/nkos/nkostype#taxonomy
Has format
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/ncbitaxon.owl
Representation language*
OWL See more...
Syntax
http://www.w3.org/ns/formats/Turtle
http://www.w3.org/ns/formats/Turtle
Homepage
https://www.ncbi.nlm.nih.gov/
https://www.ncbi.nlm.nih.gov/
Other identifier
https://doi.org/10.1093/nar/gki062
https://doi.org/10.1093/nar/gki062
Indexed or included in catalog or repository
http://aber-owl.net/ontology/NCBITAXON
http://aber-owl.net/ontology/NCBITAXON
http://www.ebi.ac.uk/ols/ontologies/ncbitaxon
http://www.ebi.ac.uk/ols/ontologies/ncbitaxon
http://www.obofoundry.org/ontology/ncbitaxon.html
http://www.obofoundry.org/ontology/ncbitaxon.html
http://www.ontobee.org/ontology/NCBITaxon
http://www.ontobee.org/ontology/NCBITaxon
https://agroportal.lirmm.fr/
https://agroportal.lirmm.fr/
https://bioportal.bioontology.org/ontologies/NCBITAXON
https://bioportal.bioontology.org/ontologies/NCBITAXON
https://biosharing.org/bsg-s000154
https://biosharing.org/bsg-s000154
https://lod-cloud.net/dataset/bioportal-ncbitaxon
https://lod-cloud.net/dataset/bioportal-ncbitaxon
https://vest.agrisemantics.org/content/national-center-biotechnology-information-ncbi-organismal-classification
https://vest.agrisemantics.org/content/national-center-biotechnology-information-ncbi-organismal-classification
Has equivalences with
https://data.agroportal.lirmm.fr/ontologies/CL
https://data.agroportal.lirmm.fr/ontologies/CL
https://data.agroportal.lirmm.fr/ontologies/EO
https://data.agroportal.lirmm.fr/ontologies/EO
https://data.agroportal.lirmm.fr/ontologies/FOODON
https://data.agroportal.lirmm.fr/ontologies/FOODON
https://data.agroportal.lirmm.fr/ontologies/GR-TAX
https://data.agroportal.lirmm.fr/ontologies/GR-TAX
https://data.agroportal.lirmm.fr/ontologies/PECO
https://data.agroportal.lirmm.fr/ontologies/PECO
Is format of
https://www.ncbi.nlm.nih.gov/taxonomy
https://www.ncbi.nlm.nih.gov/taxonomy
Generic type
http://omv.ontoware.org/2005/05/ontology#DomainOntology
http://omv.ontoware.org/2005/05/ontology#DomainOntology
Logo
https://www.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/4117326/img/28977
https://www.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/4117326/img/28977
Modification date
November 6, 2023
Object modification date property
http://purl.org/dc/elements/1.1/modified
http://purl.org/dc/elements/1.1/modified
More permissions
Information that is created by or for the US government on this site is within the public domain. Public domain information on the National Library of Medicine (NLM) Web pages may be freely distributed and copied. However, it is requested that in any subsequent use of this work, NLM be given appropriate acknowledgment. See more...
Natural language
Notes
RDF Version of the UMLS ontology NCBI; converted with the UMLS2RDF tool (https://github.com/ncbo/umls2rdf), developed by the NCBO project. See more...
Root of obsolete branch
http://www.geneontology.org/formats/oboInOwl#ObsoleteClass
http://www.geneontology.org/formats/oboInOwl#ObsoleteClass
Preferred namespace prefix
ncbitaxon See more...
Preferred namespace URI
http://purl.obolibrary.org/obo/
http://purl.obolibrary.org/obo/
Creation date*
August 27, 2023
Repository
https://github.com/obophenotype/ncbitaxon
https://github.com/obophenotype/ncbitaxon
Status*
production See more...
URI Lookup Endpoint
http://data.agroportal.lirmm.fr/search?ontologies=NCBITAXON&require_exact_match=true&q=
http://data.agroportal.lirmm.fr/search?ontologies=NCBITAXON&require_exact_match=true&q=
Imports
http://www.w3.org/2004/02/skos/core
http://www.w3.org/2004/02/skos/core
Version information
2023ab See more...

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