- Get all the children of a given term.
# Name: get_labeled_children
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_U0000000: the term for which the children will be found
# Function: returns the children of the query-term
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_U0000000>
select ?child ?name ?subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
?child default_ontology:is_a query_term_id:.
?child rdfs:label ?name.
?child rdf:type ?subnamespace.
}
- Get all the parents of a given term.
# Name: get_labeled_parents
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_B0000000: the term for which the parents will be found
# Function: returns the labeled parent terms of CCO_B0000000
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_B0000000>
select ?parent ?name ?subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
query_term_id: default_ontology:is_a ?parent.
?parent rdfs:label ?name.
?parent rdf:type ?subnamespace.
}
- Google the ontology: search trough all the content on one or more strings.
# Name: search_labeled_terms_on_properties
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: cell: the first search-string
# Parameter: activity: the second search-string
# Function: returns all the labeled terms for which a property -the name, definition, synonym or comment- contains 'cell' and 'activity'
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 ?term_id ?name ?subnamespace ?term_property ?found_string
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
filter regex(?found_string, "cell")
filter regex(?found_string, "activity")?term_id rdfs:label ?name.
?term_id rdf:type ?subnamespace.
{
?term_id ?term_property ?found_string.
?term_id rdfs:label ?found_string.
}
union
{
?term_id ?term_property ?a.
?term_id default_ontology:Definition ?a.
?a default_ontology:def ?found_string.
}
union
{
?term_id ?term_property ?a.
?term_id default_ontology:synonym ?a.
?a default_ontology:syn ?found_string.
}
union
{
?term_id ?term_property ?found_string.
?term_id rdfs:comment ?found_string.
}
}
order by ?term_id
- Search on the names of the terms with one or more strings.
# Name: search_labeled_terms_on_name
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: cell: the first search-string
# Parameter: activity: the second search-string
# Function: returns all the labeled terms for which the name contains 'cell' and 'activity'
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
select ?term_id ?name ?subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
?term_id rdfs:label ?name.
?term_id rdf:type ?subnamespace.
filter regex(?name, "cell")
filter regex(?name, "activity")
}
- Get all the neighbor terms of a given term.
# Name: get_labeled_neighborhood
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_B0002494: the term for which you get the neighboring terms and the relations to them
# Function: returns the labeled neighborhood of a term
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
prefix query_term_id:<http://www.cellcycleontology.org/ontology/rdf/CCO#CCO_B0002494>
select ?outward_arrow ?object_neighbour ?object_name ?object_subnamespace ?inward_arrow ?subject_neighbour ?subject_name ?subject_subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
{
query_term_id: ?outward_arrow ?object_neighbour.
?object_neighbour rdf:type ?object_subnamespace.
?object_neighbour rdfs:label ?object_name.
}
union{
?subject_neighbour ?inward_arrow query_term_id:.
?subject_neighbour rdf:type ?subject_subnamespace.
?subject_neighbour rdfs:label ?subject_name.
}
}
- Get all the properties, like definition, synonyms, etc., of a given term.
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_B0002268: the term for which you want the properties
# Function: returns the properties of a given term
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 ?name ?subnamespace ?definition ?dbname_def_xref ?accession_def_xref ?organism ?comment ?synonym ?scope ?dbname_syn_xref ?accession_syn_xref ?dbname_term_xref ?accession_term_xref
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where{
{query_term_id: rdfs:label ?name}
union{
query_term_id: rdf:type ?subnamespace
}
union{
query_term_id: default_ontology:Definition ?a.
{?a default_ontology:def ?definition.}
union{
optional{
?a default_ontology:DbXref ?b.
?b default_ontology:dbname ?dbname_def_xref.
?b default_ontology:acc ?accession_def_xref.
}
}
}
union
{
query_term_id: default_ontology:belongs_to ?organism_id.
?organism_id rdf:type default_ontology:taxon.
?organism_id rdfs:label ?organism.
}
union
{query_term_id: rdfs:comment ?comment}
union{
query_term_id: default_ontology:synonym ?a.
?a default_ontology:syn ?synonym.
optional{?a default_ontology:scope ?scope.}
optional{
?a default_ontology:DbXref ?b.
?b default_ontology:dbname ?dbname_syn_xref.
?b default_ontology:acc ?accession_syn_xref.
}
}
union{
query_term_id: default_ontology:xref ?a.
?a default_ontology:dbname ?dbname_term_xref.
?a default_ontology:acc ?accession_term_xref.
}
}
- Get a list of all the relation types that are used in the ontology.
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Function: returns the relationship types held by the default ontology
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select distinct ?relationship_type
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
?s ?relationship_type ?o.
?s rdf:type ?a.
?o rdf:type ?b.
}
- Get the long list of all the terms in the ontology.
# Name: get_labeled_ids_of_ontology
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Function: returns all the labeled id's of the queried ontology
prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
select ?id ?name ?subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
?id rdf:type ?subnamespace.
?id rdfs:label ?name.
}
order by ?id
- Get the root term(s) of the ontology.
# Name: get_labeled_root_of_ontology
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Function: returns the labeled root of the default ontology (all the terms without parents)
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 ?root ?name ?subnamespace
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where{
?root rdf:type ?subnamespace.
?root rdfs:label ?name.
optional{?root default_ontology:is_a ?b}.
filter(!bound(?b))
}
- Get the hierarchy to the root for a given term.
# Name: get_labeled_hierarchy_to_root
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_T0000004: the term for which you will get the hierarchy to the root
# Function: returns all the possible labeled subsumption paths to the root
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_T0000004>
select *
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
optional{
query_term_id: default_ontology:is_a ?n1 .
?n1 rdfs:label ?n1_name.
?n1 rdf:type ?n1_subnamespace.
}
optional{
?n1 default_ontology:is_a ?n2 .
?n2 rdfs:label ?n2_name.
?n2 rdf:type ?n2_subnamespace.
}
optional{
?n2 default_ontology:is_a ?n3 .
?n3 rdfs:label ?n3_name.
?n3 rdf:type ?n3_subnamespace.
}
optional{
?n3 default_ontology:is_a ?n4 .
?n4 rdfs:label ?n4_name.
?n4 rdf:type ?n4_subnamespace.
}
optional{
?n4 default_ontology:is_a ?n5 .
?n5 rdfs:label ?n5_name.
?n5 rdf:type ?n5_subnamespace.
}
optional{
?n5 default_ontology:is_a ?n6 .
?n6 rdfs:label ?n6_name.
?n6 rdf:type ?n6_subnamespace.
}
optional{
?n6 default_ontology:is_a ?n7 .
?n7 rdfs:label ?n7_name.
?n7 rdf:type ?n7_subnamespace.
}
optional{
?n7 default_ontology:is_a ?n8 .
?n8 rdfs:label ?n8_name.
?n8 rdf:type ?n8_subnamespace.
}
optional{
?n8 default_ontology:is_a ?n9 .
?n9 rdfs:label ?n9_name.
?n9 rdf:type ?n9_subnamespace.
}
optional{
?n9 default_ontology:is_a ?n10 .
?n10 rdfs:label ?n10_name.
?n10 rdf:type ?n10_subnamespace.
}
optional{
?n10 default_ontology:is_a ?n11 .
?n11 rdfs:label ?n11_name.
?n11 rdf:type ?n11_subnamespace.
}
optional{
?n11 default_ontology:is_a ?n12 .
?n12 rdfs:label ?n12_name.
?n12 rdf:type ?n12_subnamespace.
}
optional{
?n12 default_ontology:is_a ?n13 .
?n13 rdfs:label ?n13_name.
?n13 rdf:type ?n13_subnamespace.
}
optional{
?n13 default_ontology:is_a ?n14 .
?n14 rdfs:label ?n14_name.
?n14 rdf:type ?n14_subnamespace.
}
optional{
?n14 default_ontology:is_a ?n15 .
?n15 rdfs:label ?n15_name.
?n15 rdf:type ?n15_subnamespace.
}
optional{
?n15 default_ontology:is_a ?n16 .
?n16 rdfs:label ?n16_name.
?n16 rdf:type ?n16_subnamespace.
}
optional{
?n16 default_ontology:is_a ?n17 .
?n17 rdfs:label ?n17_name.
?n17 rdf:type ?n17_subnamespace.
}
optional{
?n17 default_ontology:is_a ?n18 .
?n18 rdfs:label ?n18_name.
?n18 rdf:type ?n18_subnamespace.
}
optional{
?n18 default_ontology:is_a ?n19 .
?n19 rdfs:label ?n19_name.
?n19 rdf:type ?n19_subnamespace.
}
optional{
?n19 default_ontology:is_a ?n20 .
?n20 rdfs:label ?n20_name.
?n20 rdf:type ?n20_subnamespace.
}
optional{
?n20 default_ontology:is_a ?n21 .
?n21 rdfs:label ?n21_name.
?n21 rdf:type ?n21_subnamespace.
}
optional{
?n21 default_ontology:is_a ?n22 .
?n22 rdfs:label ?n22_name.
?n22 rdf:type ?n22_subnamespace.
}
optional{
?n22 default_ontology:is_a ?n23 .
?n23 rdfs:label ?n23_name.
?n23 rdf:type ?n23_subnamespace.
}
optional{
?n23 default_ontology:is_a ?n24 .
?n24 rdfs:label ?n24_name.
?n24 rdf:type ?n24_subnamespace.
}
optional{
?n24 default_ontology:is_a ?n25 .
?n25 rdfs:label ?n25_name.
?n25 rdf:type ?n25_subnamespace.
}
optional{
?n25 default_ontology:is_a ?n26 .
?n26 rdfs:label ?n26_name.
?n26 rdf:type ?n26_subnamespace.
}
optional{
?n26 default_ontology:is_a ?n27 .
?n27 rdfs:label ?n27_name.
?n27 rdf:type ?n27_subnamespace.
}
optional{
?n27 default_ontology:is_a ?n28 .
?n28 rdfs:label ?n28_name.
?n28 rdf:type ?n28_subnamespace.
}
optional{
?n28 default_ontology:is_a ?n29 .
?n29 rdfs:label ?n29_name.
?n29 rdf:type ?n29_subnamespace.
}
optional{
?n29 default_ontology:is_a ?n30 .
?n30 rdfs:label ?n30_name.
?n30 rdf:type ?n30_subnamespace.
}
optional{
?n30 default_ontology:is_a ?n31 .
?n31 rdfs:label ?n31_name.
?n31 rdf:type ?n31_subnamespace.
}
optional{
?n31 default_ontology:is_a ?n32 .
?n32 rdfs:label ?n32_name.
?n32 rdf:type ?n32_subnamespace.
}
optional{
?n32 default_ontology:is_a ?n33 .
?n33 rdfs:label ?n33_name.
?n33 rdf:type ?n33_subnamespace.
}
optional{
?n33 default_ontology:is_a ?n34 .
?n34 rdfs:label ?n34_name.
?n34 rdf:type ?n34_subnamespace.
}
optional{
?n34 default_ontology:is_a ?n35 .
?n35 rdfs:label ?n35_name.
?n35 rdf:type ?n35_subnamespace.
}
optional{
?n35 default_ontology:is_a ?n36 .
?n36 rdfs:label ?n36_name.
?n36 rdf:type ?n36_subnamespace.
}
optional{
?n36 default_ontology:is_a ?n37 .
?n37 rdfs:label ?n37_name.
?n37 rdf:type ?n37_subnamespace.
}
}
- Get the hierarchy above a certain term for a given transitive relation type.
# Name: get_labeled_hierarchy_by_relation_type
# Parameter: http://www.cellcycleontology.org/ontology/rdf/CCO: the default ontology URI
# Parameter: CCO_P0000192: the term for which you will get the hierarchy to the root
# Parameter: part_of: the transitive relation type along which you want the upstream hierarchy
# Function: returns all the possible labeled upstream paths for a given term and a given relation type
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_relation_id:<http://www.cellcycleontology.org/ontology/rdf/CCO#part_of>
prefix query_term_id:<http://www.cellcycleontology.org/ontology/rdf/CCO#CCO_P0000192>
select *
from <http://www.cellcycleontology.org/ontology/rdf/CCO>
where {
optional{
query_term_id: query_relation_id: ?n1 .
?n1 rdfs:label ?n1_name.
?n1 rdf:type ?n1_subnamespace.
}
optional{
?n1 query_relation_id: ?n2 .
?n2 rdfs:label ?n2_name.
?n2 rdf:type ?n2_subnamespace.
}
optional{
?n2 query_relation_id: ?n3 .
?n3 rdfs:label ?n3_name.
?n3 rdf:type ?n3_subnamespace.
}
optional{
?n3 query_relation_id: ?n4 .
?n4 rdfs:label ?n4_name.
?n4 rdf:type ?n4_subnamespace.
}
optional{
?n4 query_relation_id: ?n5 .
?n5 rdfs:label ?n5_name.
?n5 rdf:type ?n5_subnamespace.
}
optional{
?n5 query_relation_id: ?n6 .
?n6 rdfs:label ?n6_name.
?n6 rdf:type ?n6_subnamespace.
}
optional{
?n6 query_relation_id: ?n7 .
?n7 rdfs:label ?n7_name.
?n7 rdf:type ?n7_subnamespace.
}
optional{
?n7 query_relation_id: ?n8 .
?n8 rdfs:label ?n8_name.
?n8 rdf:type ?n8_subnamespace.
}
optional{
?n8 query_relation_id: ?n9 .
?n9 rdfs:label ?n9_name.
?n9 rdf:type ?n9_subnamespace.
}
optional{
?n9 query_relation_id: ?n10 .
?n10 rdfs:label ?n10_name.
?n10 rdf:type ?n10_subnamespace.
}
optional{
?n10 query_relation_id: ?n11 .
?n11 rdfs:label ?n11_name.
?n11 rdf:type ?n11_subnamespace.
}
optional{
?n11 query_relation_id: ?n12 .
?n12 rdfs:label ?n12_name.
?n12 rdf:type ?n12_subnamespace.
}
optional{
?n12 query_relation_id: ?n13 .
?n13 rdfs:label ?n13_name.
?n13 rdf:type ?n13_subnamespace.
}
optional{
?n13 query_relation_id: ?n14 .
?n14 rdfs:label ?n14_name.
?n14 rdf:type ?n14_subnamespace.
}
optional{
?n14 query_relation_id: ?n15 .
?n15 rdfs:label ?n15_name.
?n15 rdf:type ?n15_subnamespace.
}
optional{
?n15 query_relation_id: ?n16 .
?n16 rdfs:label ?n16_name.
?n16 rdf:type ?n16_subnamespace.
}
optional{
?n16 query_relation_id: ?n17 .
?n17 rdfs:label ?n17_name.
?n17 rdf:type ?n17_subnamespace.
}
optional{
?n17 query_relation_id: ?n18 .
?n18 rdfs:label ?n18_name.
?n18 rdf:type ?n18_subnamespace.
}
optional{
?n18 query_relation_id: ?n19 .
?n19 rdfs:label ?n19_name.
?n19 rdf:type ?n19_subnamespace.
}
optional{
?n19 query_relation_id: ?n20 .
?n20 rdfs:label ?n20_name.
?n20 rdf:type ?n20_subnamespace.
}
optional{
?n20 query_relation_id: ?n21 .
?n21 rdfs:label ?n21_name.
?n21 rdf:type ?n21_subnamespace.
}
optional{
?n21 query_relation_id: ?n22 .
?n22 rdfs:label ?n22_name.
?n22 rdf:type ?n22_subnamespace.
}
optional{
?n22 query_relation_id: ?n23 .
?n23 rdfs:label ?n23_name.
?n23 rdf:type ?n23_subnamespace.
}
optional{
?n23 query_relation_id: ?n24 .
?n24 rdfs:label ?n24_name.
?n24 rdf:type ?n24_subnamespace.
}
optional{
?n24 query_relation_id: ?n25 .
?n25 rdfs:label ?n25_name.
?n25 rdf:type ?n25_subnamespace.
}
optional{
?n25 query_relation_id: ?n26 .
?n26 rdfs:label ?n26_name.
?n26 rdf:type ?n26_subnamespace.
}
optional{
?n26 query_relation_id: ?n27 .
?n27 rdfs:label ?n27_name.
?n27 rdf:type ?n27_subnamespace.
}
optional{
?n27 query_relation_id: ?n28 .
?n28 rdfs:label ?n28_name.
?n28 rdf:type ?n28_subnamespace.
}
optional{
?n28 query_relation_id: ?n29 .
?n29 rdfs:label ?n29_name.
?n29 rdf:type ?n29_subnamespace.
}
optional{
?n29 query_relation_id: ?n30 .
?n30 rdfs:label ?n30_name.
?n30 rdf:type ?n30_subnamespace.
}
optional{
?n30 query_relation_id: ?n31 .
?n31 rdfs:label ?n31_name.
?n31 rdf:type ?n31_subnamespace.
}
optional{
?n31 query_relation_id: ?n32 .
?n32 rdfs:label ?n32_name.
?n32 rdf:type ?n32_subnamespace.
}
optional{
?n32 query_relation_id: ?n33 .
?n33 rdfs:label ?n33_name.
?n33 rdf:type ?n33_subnamespace.
}
optional{
?n33 query_relation_id: ?n34 .
?n34 rdfs:label ?n34_name.
?n34 rdf:type ?n34_subnamespace.
}
optional{
?n34 query_relation_id: ?n35 .
?n35 rdfs:label ?n35_name.
?n35 rdf:type ?n35_subnamespace.
}
optional{
?n35 query_relation_id: ?n36 .
?n36 rdfs:label ?n36_name.
?n36 rdf:type ?n36_subnamespace.
}
optional{
?n36 query_relation_id: ?n37 .
?n37 rdfs:label ?n37_name.
?n37 rdf:type ?n37_subnamespace.
}
}