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

Prefix

gtdb

Keywords

ontology 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

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

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

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

In Collection

Synapse.org external links

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.