- Get a list of all the subnamespaces in CCO.
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Function: returns the subnamespaces of the default ontology
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select distinct ?subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where{
?a rdf:type ?subnamespace .
}
- Get all the proteins that interact with a given protein.
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_B0003247: the term for which the interacting proteins will be found
# Function: returns all the proteins that interact with a given protein
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
prefix default_ontology:<http://www.cellcycleontology.org/ontology/rdf/CCO#>
prefix query_term_id:<http://www.cellcycleontology.org/ontology/rdf/CCO#CCO_B0003247>
select ?interacting_protein ?ip_name
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
query_term_id: default_ontology:participates_in ?interaction.
?interacting_protein default_ontology:participates_in ?interaction.
?interacting_protein rdfs:label ?ip_name.
?interaction rdf:type default_ontology:interaction.
}
- Get all the orthologs of a given protein.
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_B0002268: the term for which you want the orthologs
# Function: returns all the orthologs for a given protein and the organism to which they belong
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
prefix default_ontology:<http://www.cellcycleontology.org/ontology/rdf/CCO#>
prefix query_term_id:<http://www.cellcycleontology.org/ontology/rdf/CCO#CCO_B0002268>
select ?ortholog_id ?ortholog_name ?organism_id ?organism_name
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where{
query_term_id: default_ontology:is_a ?a.
?ortholog_id default_ontology:is_a ?a.
?a rdf:type default_ontology:term.
?ortholog_id rdf:type default_ontology:protein.
?ortholog_id default_ontology:belongs_to ?organism_id.
?ortholog_id rdfs:label ?ortholog_name.
?organism_id rdfs:label ?organism_name.
filter(?ortholog_id != query_term_id:).
}
- Get the small list of organisms that are in CCO.
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Function: returns all the organisms to which terms in the ontology belong
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
prefix default_ontology:<http://www.cellcycleontology.org/ontology/rdf/CCO#>
select distinct ?organism_id ?organism_label
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where{
?a default_ontology:belongs_to ?organism_id.
?organism_id rdf:type default_ontology:taxon.
?organism_id rdfs:label ?organism_label.
}