URI*
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http://purl.bioontology.org/ontology/NCBITAXON/
http://purl.bioontology.org/ontology/NCBITAXON/
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Abstract
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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.
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Bug database
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https://github.com/obophenotype/ncbitaxon/issues
https://github.com/obophenotype/ncbitaxon/issues
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Comes from the same domain
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Contact*
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Ncbi Information (info@ncbi.nlm.nih.gov)
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Object creation date property
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http://purl.org/dc/elements/1.1/created
http://purl.org/dc/elements/1.1/created
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Submission date
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August 27, 2023
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Deprecated
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false
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Description*
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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.
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Documentation
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https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/
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Example of resource
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http://purl.bioontology.org/ontology/NCBITAXON/201174
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Subject
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https://data.agroportal.lirmm.fr/categories/TAX
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Formality level
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http://w3id.org/nkos/nkostype#taxonomy
http://w3id.org/nkos/nkostype#taxonomy
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Has format
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http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/ncbitaxon.owl
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Representation language*
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OWL
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Syntax
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http://www.w3.org/ns/formats/Turtle
http://www.w3.org/ns/formats/Turtle
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Homepage
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https://www.ncbi.nlm.nih.gov/
https://www.ncbi.nlm.nih.gov/
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Other identifier
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https://doi.org/10.1093/nar/gki062
https://doi.org/10.1093/nar/gki062
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Indexed or included in catalog or repository
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https://lod-cloud.net/dataset/bioportal-ncbitaxon
https://lod-cloud.net/dataset/bioportal-ncbitaxon
http://www.ebi.ac.uk/ols/ontologies/ncbitaxon
http://www.ebi.ac.uk/ols/ontologies/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
https://agroportal.lirmm.fr/
agroportal.lirmm.fr
https://bioportal.bioontology.org/ontologies/NCBITAXON
https://bioportal.bioontology.org/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://biosharing.org/bsg-s000154
https://biosharing.org/bsg-s000154
http://aber-owl.net/ontology/NCBITAXON
http://aber-owl.net/ontology/NCBITAXON
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Has equivalences with
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Is format of
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https://www.ncbi.nlm.nih.gov/taxonomy
https://www.ncbi.nlm.nih.gov/taxonomy
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Generic type
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http://omv.ontoware.org/2005/05/ontology#DomainOntology
http://omv.ontoware.org/2005/05/ontology#DomainOntology
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Logo
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https://www.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/4117326/img/28977
https://www.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/4117326/img/28977
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Modification date
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November 6, 2023
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Object modification date property
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http://purl.org/dc/elements/1.1/modified
http://purl.org/dc/elements/1.1/modified
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More permissions
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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.
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Natural language
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Notes
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RDF Version of the UMLS ontology NCBI; converted with the UMLS2RDF tool (https://github.com/ncbo/umls2rdf), developed by the NCBO project.
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Root of obsolete branch
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http://www.geneontology.org/formats/oboInOwl#ObsoleteClass
http://www.geneontology.org/formats/oboInOwl#ObsoleteClass
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Preferred namespace prefix
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ncbitaxon
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Preferred namespace URI
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http://purl.obolibrary.org/obo/
http://purl.obolibrary.org/obo/
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Creation date*
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August 27, 2023
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Repository
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https://github.com/obophenotype/ncbitaxon
https://github.com/obophenotype/ncbitaxon
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Status*
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production
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URI Lookup Endpoint
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http://agroportal.lirmm.fr/search?ontologies=NCBITAXON&require_exact_match=true&q=
search?ontologies=NCBITAXON&require_exact_match=true&q=
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Imports
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http://www.w3.org/2004/02/skos/core
http://www.w3.org/2004/02/skos/core
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Version information
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2023ab
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