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National Center for Biotechnology Information (NCBI) Organismal Classification

Last uploaded: January 11, 2022
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Details
Acronym NCBITAXON
Visibility Public
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.
Status Production
Format UMLS
Contact NCBI information, info@ncbi.nlm.nih.gov
Categories Taxonomic Classifications of Organisms
Groups OBO Foundry, Rice Data Interoperability working group
Additional Metadata
abstractThe 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.
From the same domain thanGR-TAX, TAXREF-LD
copyright HolderNLM (https://www.nlm.nih.gov/)
deprecatedfalse
endorsed By
endpoint
example Identifierhttp://purl.bioontology.org/ontology/NCBITAXON/201174
has Domainhttp://data.agroportal.lirmm.fr/categories/TAX
has Formality Levelhttp://w3id.org/nkos/nkostype#taxonomy
has Formathttp://purl.obolibrary.org/obo/ncbitaxon.owl
Ontology Syntaxhttp://www.w3.org/ns/formats/Turtle
has Prior VersionNCBITAXON/submissions/6
is Aligned ToEO, GR-TAX, CL, FOODON, PECO
is Format Ofhttps://www.ncbi.nlm.nih.gov/taxonomy
is Of Typehttp://omv.ontoware.org/2005/05/ontology#DomainOntology
Metadata vocabulary usedlocal:local
modification Date2021-11-01T00:00:00+00:00
more PermissionsInformation 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.
Natural Language
preferred Namespace Prefixncbitaxon
publisherNCBI (https://www.ncbi.nlm.nih.gov/)
Release date2021-06-13T00:00:00+00:00
URI Lookup Endpointhttp://data.agroportal.lirmm.fr/search?ontologies=NCBITAXON&require_exact_match=true&q=
use Importslocal:local
version2021AB
Submissions
Version
Released
Modified
Uploaded
Downloads
2021AB (Archived) 06/13/2021 11/01/2021 01/11/2022 RDF/TTL
2021AA (Uploaded, Error Rdf) 06/13/2021 05/03/2021 01/11/2022 RDF/TTL
2020AB (Uploaded) 11/02/2020 03/26/2021 RDF/TTL | CSV
2020AA (Uploaded) 05/05/2020 03/25/2021 RDF/TTL
2019AB (Parsed, Indexed, Metrics, Annotator) 11/04/2019 05/20/2020 RDF/TTL
2018AA (Archived) 05/07/2018 05/19/2020 RDF/TTL
2017AB (Uploaded) 11/06/2017 05/18/2020 RDF/TTL
2016AB (Archived) 11/08/2016 05/18/2020 RDF/TTL
2015AA (Archived) 06/09/2015 06/23/2015 RDF/TTL
more...
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EBI Ontology LookupBioPortalVEST RegistryThe OBO FoundryOntobeeBioSharingAberOWL
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