Registry Genome Taxonomy Database

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardized microbial taxonomy based on genome phylogeny.

Prefix: gtdb
Keywords: gene genome microbiology ontology phylogenetics taxonomy
License: CC-BY-SA-4.0
Links: Homepage OBO OWL OBO JSON Request Discussion
Publications: 2021 GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy; 2021 A standardized archaeal taxonomy for the Genome Taxonomy Database; 2020 A complete domain-to-species taxonomy for Bacteria and Archaea; 2018 A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life; 2026 GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes

Identifier Standards

Pattern for Local Unique Identifiers: Local identifiers in Genome Taxonomy Database should match this regular expression:
^[cdfgops]__\w+\S+$
Example Local Unique Identifier: g__Prochlorococcus_A Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Genome Taxonomy Database should match this regular expression:
^gtdb:[cdfgops]__\w+\S+$
Example CURIE: gtdb:g__Prochlorococcus_A

Contacts

Contact: Donovan Parks 0000-0001-6662-9010 donovan-h-parks
Contributors: submitter AJ Ireland 0000-0003-1982-9065 ialarmedalien
Reviewer: Charles Tapley Hoyt 0000-0003-4423-4370 cthoyt

Ontology

A summary of the relations in the Bioregistry schema can be found here.

In Collection (1): Synapse.org external links

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 1 mapping to an external registry.

Registry Name	Registry Metaprefix	External Prefix	Curate
FAIRSharing	`fairsharing`	`FAIRsharing.ce56c9`

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier g__Prochlorococcus_A is used to demonstrate the providers available for Genome Taxonomy Database. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Provider Name	Provider Code	URI
Genome Taxonomy Database	`gtdb`	https://gtdb.ecogenomic.org/tree?r=g__Prochlorococcus_A
Bioregistry	`bioregistry`	https://bioregistry.io/gtdb:g__Prochlorococcus_A

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("gtdb")
'Genome Taxonomy Database'

Get the license:

>>> import bioregistry as br
>>> br.get_license("gtdb")
'CC-BY-SA-4.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("gtdb")
'https://gtdb.ecogenomic.org'

Get the OBO download link:

>>> import bioregistry as br
>>> br.get_obo_download("gtdb")
'https://w3id.org/biopragmatics/resources/gtdb/gtdb.obo.gz'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("gtdb")
'https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl'

Get the JSON download link:

>>> import bioregistry as br
>>> br.get_json_download("gtdb")
'https://w3id.org/biopragmatics/resources/gtdb/gtdb.json.gz'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("gtdb")
'Donovan Parks'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("gtdb")
'donovan.parks@gmail.com'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("gtdb")
'donovan-h-parks'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("gtdb")
'0000-0001-6662-9010'