Registry NCBI Taxonomy

The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.

Prefix

ncbitaxon

Preferred Prefix

NCBITaxon

Alternative Prefixes

TAX taxid TaxonomyID taxon NCBITaxon NCBI Taxonomy uniprot.taxonomy NCBI_Taxon_ID NCBI_taxid taxonomy

Keywords

classification dna life science obo ontology phylogenetics protein structure taxonomy

Version

2022-08-18

License

CC0-1.0

Links

Homepage Repository OBO OWL OBO JSON

Contact

Frederic Bastian 0000-0002-9415-5104 fbastian

Identifier Space Owner

National Center for Biotechnology Information

Pattern for Local Unique Identifiers

Local identifiers in NCBI Taxonomy should match this regular expression:
^\d+$

Example Local Unique Identifier

2170610 Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from NCBI Taxonomy should match this regular expression:
^ncbitaxon:\d+$

Example CURIE

ncbitaxon:2170610

Publications

2020 NCBI Taxonomy: a comprehensive update on curation, resources and tools.
2018 GenBank.
2011 The NCBI Taxonomy database.

Ontology

Provided By: cutg virmirdb virushostdb
Appears In (15) (bioregistry.schema:0000018 ): AGRO CHIRO CL CLO ECTO ENVO FOODON GENEPIO GO HSO MCO ONS PCL PCO VBO

Metaregistry NCBI Taxonomy

The metaregistry provides mappings between the Bioregistry and other registries. There are 19 mappings to external registries for ncbitaxon with 10 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
AberOWL	`aberowl`	`NCBITAXON`
AgroPortal	`agroportal`	`NCBITAXON`
BARTOC	`bartoc`	`509`
BioContext	`biocontext`	`TAXONOMY`
BioPortal	`bioportal`	`NCBITAXON`
Cellosaurus	`cellosaurus`	`NCBI_TaxID`
EDAM	`edam`	`1179`
FAIRSharing	`fairsharing`	`FAIRsharing.fj07xj`
GO	`go`	`taxon`
HL7	`hl7`	`2.16.840.1.113883.6.205`
Identifiers.org	`miriam`	`taxonomy`
N2T	`n2t`	`taxonomy`
NCBI	`ncbi`	`taxon`
OBO Foundry	`obofoundry`	`ncbitaxon`
OLS	`ols`	`ncbitaxon`
OntoBee	`ontobee`	`NCBITaxon`
Prefix Commons	`prefixcommons`	`taxonomy`
re3data	`re3data`	`r3d100010415`
Wikidata	`wikidata`	`P685`

Providers

Providers are various services that resolve CURIEs to URLs. The example CURIE ncbitaxon:2170610 is used to demonstrate the provides available for ncbitaxon. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.

Name	Metaprefix	URI
NCBI Taxonomy	`ncbitaxon`	https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2170610
Bioregistry	`bioregistry`	https://bioregistry.io/ncbitaxon:2170610
Identifiers.org	`miriam`	https://identifiers.org/taxonomy:2170610
OBO Foundry	`obofoundry`	http://purl.obolibrary.org/obo/NCBITaxon_2170610
Ontology Lookup Service	`ols`	https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?iri=http://purl.obolibrary.org/obo/NCBITaxon_2170610
Name-to-Thing	`n2t`	https://n2t.net/taxonomy:2170610
BioPortal Prefixes	`bioportal`	https://bioportal.bioontology.org/ontologies/NCBITAXON/?p=classes&conceptid=http://purl.obolibrary.org/obo/NCBITaxon_2170610

Extra Providers

Additional providers curated in the Bioregistry are listed here.

Code	Name	URL
`CURATOR_REVIEW`	Taxonomy through UniProt PURL	https://purl.uniprot.org/taxonomy/2170610
`CURATOR_REVIEW`	Bio2RDF	https://bio2rdf.org/taxonomy:2170610
`bio2rdf`	Bio2RDF	http://bio2rdf.org/taxonomy:2170610
`ebi`	European Nucleotide Archive (ENA)	https://www.ebi.ac.uk/ena/data/view/Taxon:2170610
`scholia`	Scholia	https://scholia.toolforge.org/ncbi-taxon/2170610

Normalize prefixes. This can be any capitalization or punctuation variant of the synonyms listed below.

>>> import bioregistry as br
>>> br.normalize_prefix("TAX")
'ncbitaxon'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("ncbitaxon")
{'TAX', 'taxid', 'TaxonomyID', 'taxon', 'NCBITaxon', 'NCBI Taxonomy', 'uniprot.taxonomy', 'NCBI_Taxon_ID', 'NCBI_taxid', 'taxonomy'}

Get the version:

>>> import bioregistry as br
>>> br.get_version("ncbitaxon")
'2022-08-18'

Get the license:

>>> import bioregistry as br
>>> br.get_license("ncbitaxon")
'CC0-1.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("ncbitaxon")
'https://github.com/obophenotype/ncbitaxon'

Get the repository:

>>> import bioregistry as br
>>> br.get_repository("ncbitaxon")
'https://github.com/obophenotype/ncbitaxon'

Get the OBO download link:

>>> import bioregistry as br
>>> br.get_obo_download("ncbitaxon")
'http://purl.obolibrary.org/obo/ncbitaxon.obo'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("ncbitaxon")
'http://purl.obolibrary.org/obo/ncbitaxon.owl'

Get the JSON download link:

>>> import bioregistry as br
>>> br.get_json_download("ncbitaxon")
'http://purl.obolibrary.org/obo/ncbitaxon.json'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("ncbitaxon")
'Frederic Bastian'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("ncbitaxon")
'frederic.bastian@unil.ch'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("ncbitaxon")
'fbastian'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("ncbitaxon")
'0000-0002-9415-5104'