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Update queries for taxon aspect
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-60
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+58
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‎scholia/app/templates/taxon_co-occurring-taxa.sparql‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,9 @@
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{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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#title: Taxa that co-occur with the target taxon in the literature
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX bd: <http://www.bigdata.com/rdf#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX wdt: <http://www.wikidata.org/prop/direct/>
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PREFIX wikibase: <http://wikiba.se/ontology#>
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SELECT ?count (CONCAT("/topics/", SUBSTR(STR(target:),32), ",", SUBSTR(STR(?taxon),32)) AS ?countUrl) ?taxon ?taxonLabel (CONCAT("/taxon/", SUBSTR(STR(?taxon),32)) AS ?taxonUrl) ?example_work ?example_workLabel (CONCAT("/work/", SUBSTR(STR(?example_work),32)) AS ?example_workUrl) WHERE {
@@ -18,7 +21,7 @@ SELECT ?count (CONCAT("/topics/", SUBSTR(STR(target:),32), ",", SUBSTR(STR(?taxo
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}
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GROUP BY ?taxon
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}
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# SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en" . }
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{{ sparql_helpers.labels(["?taxon", "?example_work"], languages) }}
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}
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ORDER BY DESC(?count)
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LIMIT 200

‎scholia/app/templates/taxon_genome.sparql‎

Lines changed: 7 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,14 @@
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{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX bd: <http://www.bigdata.com/rdf#>
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PREFIX wd: <http://www.wikidata.org/entity/>
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PREFIX wdt: <http://www.wikidata.org/prop/direct/>
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PREFIX wikibase: <http://wikiba.se/ontology#>
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SELECT ?gene ?geneLabel ?geneDescription ?chromosome ?chromosomeLabel ?chromosomeDescription {
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{
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SELECT ?gene ?chromosome WHERE {
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?gene wdt:P31 wd:Q7187 ;
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wdt:P703 target: ;
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wdt:P1057 ?chromosome .
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}
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}
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# SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". }
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?gene wdt:P31 wd:Q7187 ;
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wdt:P703 target: ;
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wdt:P1057 ?chromosome .
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{{ sparql_helpers.labels(["?gene", "?chromosome"], languages) }}
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{{ sparql_helpers.descriptions(["?gene", "?chromosome"], languages) }}
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}

‎scholia/app/templates/taxon_identifiers.sparql‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,5 @@
1+
{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX bd: <http://www.bigdata.com/rdf#>
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PREFIX wd: <http://www.wikidata.org/entity/>
@@ -44,7 +46,8 @@ SELECT ?Identifier ?IdentifierLabel ?id (SAMPLE(?idUrls) AS ?idUrl) ?IdentifierD
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BIND (IRI(REPLACE(?formatterurl, '\\\\$1', STR(?id))) AS ?idUrls) .
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}
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}
47-
# SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". }
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{{ sparql_helpers.labels(["?Identifier"], languages) }}
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{{ sparql_helpers.descriptions(["?Identifier"], languages) }}
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}
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GROUP BY ?Identifier ?IdentifierLabel ?IdentifierDescription ?id
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ORDER BY ASC(?IdentifierLabel)

‎scholia/app/templates/taxon_metabolome.sparql‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,5 @@
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{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX bd: <http://www.bigdata.com/rdf#>
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PREFIX wd: <http://www.wikidata.org/entity/>
@@ -25,5 +27,6 @@ SELECT DISTINCT ?metabolite ?metaboliteLabel ?metaboliteChemicalStructure ?metab
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BIND (COALESCE(?isoSmiles, ?canSmiles) AS ?metaboliteChemicalStructure)
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}
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}
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# SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". }
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{{ sparql_helpers.labels(["?metabolite"], languages) }}
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{{ sparql_helpers.descriptions(["?metabolite"], languages) }}
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}

‎scholia/app/templates/taxon_parent-taxa.sparql‎

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Original file line numberDiff line numberDiff line change
@@ -1,16 +1,16 @@
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{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX bd: <http://www.bigdata.com/rdf#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX wdt: <http://www.wikidata.org/prop/direct/>
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PREFIX wikibase: <http://wikiba.se/ontology#>
6-
SELECT (COUNT(?middle) AS ?distance) (GROUP_CONCAT(DISTINCT ?rank_label_; SEPARATOR=", ") AS ?rank) ?parent ?parentLabel ?parentDescription {
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SELECT (COUNT(?middle) AS ?distance) (GROUP_CONCAT(DISTINCT ?rank_Label; SEPARATOR=", ") AS ?rank) ?parent ?parentLabel ?parentDescription {
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target: wdt:P171* ?middle .
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?middle wdt:P171+ ?parent .
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?parent wdt:P105 ?rank_ .
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OPTIONAL {
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?rank_ rdfs:label ?rank_label_ . FILTER (LANG(?rank_label_) = 'en')
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}
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# SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". }
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{{ sparql_helpers.labels(["?rank_", "?parent"], languages) }}
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{{ sparql_helpers.descriptions(["?parent"], languages) }}
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}
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GROUP BY ?parent ?parentLabel ?parentDescription
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ORDER BY ?distance

‎scholia/app/templates/taxon_proteome.sparql‎

Lines changed: 7 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,14 @@
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{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX bd: <http://www.bigdata.com/rdf#>
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PREFIX wd: <http://www.wikidata.org/entity/>
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PREFIX wdt: <http://www.wikidata.org/prop/direct/>
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PREFIX wikibase: <http://wikiba.se/ontology#>
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SELECT ?protein ?proteinLabel ?proteinDescription ?gene ?geneLabel {
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{
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SELECT ?protein ?gene ?chromosome WHERE {
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?protein wdt:P31 wd:Q8054 ;
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wdt:P703 target: .
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}
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}
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?protein wdt:P702 ?gene .
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# SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],mul,en". }
9+
?protein wdt:P31 wd:Q8054 ;
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wdt:P703 target: ;
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wdt:P702 ?gene.
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{{ sparql_helpers.labels(["?protein", "?gene"], languages) }}
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{{ sparql_helpers.descriptions(["?protein"], languages) }}
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}

‎scholia/app/templates/taxon_tree.sparql‎

Lines changed: 27 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -1,47 +1,38 @@
1+
{% import 'sparql-helpers.sparql' as sparql_helpers -%}
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#defaultView:Graph
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PREFIX target: <http://www.wikidata.org/entity/{{ q }}>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX wdt: <http://www.wikidata.org/prop/direct/>
5-
SELECT ?child ?childLabel ?rgb ?parent ?parentLabel WHERE {
7+
SELECT (?child_ AS ?child) ?childLabel ?rgb (?parent_ AS ?parent) ?parentLabel WHERE {
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{
7-
SELECT ?child ?rgb ?parent WHERE {
8-
{
9-
# Parent taxa
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SELECT ?child ?rgb ?parent WHERE {
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SERVICE gas:service {
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gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" ;
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gas:in target: ;
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# We should not do undirected here because this could result
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# in very big graphs.
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gas:traversalDirection "Forward" ;
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gas:out ?child ;
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gas:out1 ?depth ;
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gas:out2 ?parent1 ;
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gas:linkType wdt:P171 ;
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}
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?child wdt:P171 ?parent .
23-
BIND (IF(?child = target:,"FF0000","FFFFFF") AS ?rgb)
24-
}
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}
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UNION {
27-
# Child taxa
28-
SELECT ?child ?rgb ?parent WHERE {
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BIND (target: AS ?parent)
30-
?child wdt:P171 ?parent .
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BIND ("DDDDDD" AS ?rgb)
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}
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LIMIT 100
34-
}
35-
}
9+
# Parent taxa
10+
target: wdt:P171* ?child_ .
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?child_ wdt:P171 ?parent_ .
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BIND ("FFFFFF" AS ?rgb)
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} UNION {
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# Child taxa
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{SELECT ?child_ ?parent_ WHERE {
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BIND (target: AS ?parent_) .
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?child_ wdt:P171 ?parent_ .
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} LIMIT 100}
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BIND ("DDDDDD" AS ?rgb)
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} UNION {
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BIND (target: AS ?child_) .
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?child_ wdt:P171 ?parent_ .
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BIND ("FF0000" AS ?rgb)
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}
37-
?child rdfs:label ?child_label . FILTER (LANG(?child_label) = 'en')
38-
?parent rdfs:label ?parent_label . FILTER (LANG(?parent_label) = 'en')
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3926
OPTIONAL {
40-
?child wdt:P105/rdfs:label ?child_rank_label . FILTER (LANG(?child_rank_label) = 'en')
27+
?child_ wdt:P105 ?child_rank_ .
28+
{{ sparql_helpers.labels(["?child_rank_"], languages) }}
4129
}
4230
OPTIONAL {
43-
?parent wdt:P105/rdfs:label ?parent_rank_label . FILTER (LANG(?parent_rank_label) = 'en')
31+
?parent_ wdt:P105 ?parent_rank_ .
32+
{{ sparql_helpers.labels(["?parent_rank_"], languages) }}
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}
45-
BIND (CONCAT(?child_label, " - ", COALESCE(?child_rank_label, "???")) AS ?childLabel)
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BIND (CONCAT(?parent_label, " - ", COALESCE(?parent_rank_label, "???")) AS ?parentLabel)
34+
{{ sparql_helpers.labels(["?child_", "?parent_"], languages) }}
35+
36+
BIND (CONCAT(?child_Label, " - ", COALESCE(?child_rank_Label, "???")) AS ?childLabel)
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BIND (CONCAT(?parent_Label, " - ", COALESCE(?parent_rank_Label, "???")) AS ?parentLabel)
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}

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