GTDB
The Genome Taxonomy Database (GTDB) is a resource that provides a standardized taxonomy for bacterial and archaeal genomes based on genome phylogeny. This RDF dataset is generated by the RDF Portal based on data distributed by GTDB, representing the taxonomy and associated information in a semantic format to enable data integration and advanced querying across life science resources.
Dataset specifications
| Tags |
taxonomy
bacteria
archaea
|
| Provenance |
Third party
|
| Registration |
Added by RDF portal
|
| Data provider |
- The University of Queensland
|
| Creator |
-
Shuichi Kawashimahttps://dbcls.rois.ac.jp/
|
| Issued |
2024-06-27 |
| Licenses |
-
See licenses at https://gtdb.ecogenomic.org/licenses
|
| Version |
2024-06-27 |
| Download |
https://rdfportal.org/download/gtdb
|
| SPARQL Endpoint |
https://rdfportal.org/primary/sparql
|
Dataset statistics
- Triples
- 48602271
- Subjects
- 516026
- Properties
- 113
- Objects
- 7800464
- Classes
- 2
SPARQL example queries
# Retrieve and print the GTDB taxonomic classification for the strains corresponding to the given NCBI taxids .
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX gtdb: <http://identifiers.org/gtdb/onto/>
SELECT ?taxid ?strain ?species_label ?genus_label ?family_label ?order_label ?class_label ?phyla_label ?domain_label
WHERE {
VALUES ?taxid {"191218" "190304"}
?strain gtdb:ncbi_taxid ?taxid ;
rdfs:subClassOf ?species .
?species rdfs:label ?species_label ;
rdfs:subClassOf ?genus .
?genus rdfs:label ?genus_label ;
rdfs:subClassOf ?family .
?family rdfs:label ?family_label ;
rdfs:subClassOf ?order .
?order rdfs:label ?order_label ;
rdfs:subClassOf ?class .
?class rdfs:label ?class_label ;
rdfs:subClassOf ?phyla .
?phyla rdfs:label ?phyla_label ;
rdfs:subClassOf ?domain .
?domain rdfs:label ?domain_label .
}
LIMIT 10