Human Chromosome Ontology (HCO)
The Human Chromosome Ontology (HCO) provides simple, stable, and version-aware URIs for semantically identifying human chromosomes in different human reference genome assemblies. HCO enables RDF datasets to describe chromosome-level genomic locations consistently across reference genome versions.
Dataset specifications
| Tags |
Ontology/Terminology/Nomenclature
|
| Provenance |
Original
|
| Registration |
Submitted
|
| Data provider |
- Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics, National Institute of Genetics
|
| Creator |
-
Toshiaki KatayamaNational Institute of Genetics
|
| Issued |
2020-07-15 |
| Licenses |
-
Attribution 4.0 International (CC BY 4.0) Database Center for Life Science
|
| Version |
2020-07-15 |
| Download |
/website/download/#hco
|
| SPARQL Endpoint |
https://rdfportal.org/primary/sparql
|
Dataset statistics
- Triples
- 25646
- Subjects
- 7861
- Properties
- 18
- Objects
- 9536
- Classes
- 896
SPARQL example queries
# Retrieve a list of human chromosome classes included in HCO.
PREFIX hco: <http://identifiers.org/hco/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?chromosome_class ?label
FROM <http://rdfportal.org/dataset/hco>
WHERE {
?chromosome_class rdfs:subClassOf hco:HumanChromosome ;
rdfs:label ?label .
}
ORDER BY ?chromosome_class
# Retrieve chromosome instances and their lengths in GRCh38.
PREFIX hco: <http://identifiers.org/hco/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?chromosome ?chromosome_class ?label ?length
FROM <http://rdfportal.org/dataset/hco>
WHERE {
?chromosome rdf:type ?chromosome_class ;
hco:length ?length .
?chromosome_class rdfs:subClassOf hco:HumanChromosome ;
rdfs:label ?label .
FILTER(STRENDS(STR(?chromosome), "/GRCh38"))
}
ORDER BY ?chromosome
# Retrieve a list of reference genome builds.
PREFIX hco: <http://identifiers.org/hco/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT ?build ?label ?alt_label ?definition ?date ?length
FROM <http://rdfportal.org/dataset/hco>
WHERE {
?build rdf:type ?build_class ;
rdfs:label ?label .
OPTIONAL { ?build skos:altLabel ?alt_label . }
OPTIONAL { ?build skos:definition ?definition . }
OPTIONAL { ?build dct:date ?date . }
OPTIONAL { ?build hco:length ?length . }
VALUES ?build_class {
hco:GenomeBuild
hco:GRCh37
hco:GRCh38
}
}
ORDER BY ?build