Project:SPARQL/examples
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List all taxon items
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?item ?itemLabel WHERE {
?item ppt:P18 pp:Q2.
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
List all interaction types and RO mapping if available
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?item ?itemLabel ?roterm WHERE {
?item ppt:P18 pp:Q1.
OPTIONAL {
?item ppt:P16 ?roterm
}
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
List all body parts and GO mapping if available
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?item ?itemLabel ?goterm WHERE {
?item ppt:P18 pp:Q5.
OPTIONAL {
?item ppt:P17 ?goterm
}
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
List all analytical techniques and Wikidata mapping if available
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?item ?itemLabel ?wikidata WHERE {
?item ppt:P18 pp:Q6.
OPTIONAL {
?item ppt:P2 ?wikidata
}
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
List all interactions, optionally the localization, interaction type, and references
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
PREFIX pps: <https://ppsdb.wikibase.cloud/prop/>
PREFIX ppss: <https://ppsdb.wikibase.cloud/prop/statement/>
PREFIX ppsq: <https://ppsdb.wikibase.cloud/prop/qualifier/>
PREFIX ppsr: <https://ppsdb.wikibase.cloud/prop/reference/>
SELECT DISTINCT ?host ?hostLabel ?typeLabel ?symbiontLabel ?localizationLabel ?doi ?statedin WHERE {
?host pps:P19 ?interaction.
?interaction ppss:P19 ?symbiont.
OPTIONAL { ?interaction ppsq:P20 ?localization. }
OPTIONAL { ?interaction ppsq:P26 ?type. }
OPTIONAL {
?interaction prov:wasDerivedFrom ?refnode.
OPTIONAL { ?refnode ppsr:P27 ?doi }
OPTIONAL { ?refnode ppsr:P23 ?statedin }
}
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
Draw graph of all hosts connected to Megaira polyxenophila and their other interactions
Megaira polyxenophila Q141 is an intracellular bacterium in a wide diversity of host taxa. This query includes sub-species of Megaira polyxenophila.
#defaultView:Graph
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
PREFIX pps: <https://ppsdb.wikibase.cloud/prop/>
PREFIX ppss: <https://ppsdb.wikibase.cloud/prop/statement/>
PREFIX ppsq: <https://ppsdb.wikibase.cloud/prop/qualifier/>
SELECT DISTINCT ?host ?hostLabel ?pic ?linkto ?linktoLabel ?edgeLabel WHERE {
?host pps:P19 ?statement.
?statement ppss:P19/ppt:P29* pp:Q141 # include items with parent taxon Q141
OPTIONAL { ?statement ppsq:P20 ?edge }
OPTIONAL { ?host ppt:P19 ?linkto }
OPTIONAL { ?host ppt:P33 ?pic }
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
Maintenance queries
Generate QuickStatements to add "instance of: taxon" to items with NCBI taxon IDs
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
PREFIX pps: <https://ppsdb.wikibase.cloud/prop/>
PREFIX ppss: <https://ppsdb.wikibase.cloud/prop/statement/>
PREFIX ppsq: <https://ppsdb.wikibase.cloud/prop/qualifier/>
SELECT DISTINCT ?qid ?P18 WHERE {
?host pps:P19 ?symbiont.
FILTER NOT EXISTS {
?host ppt:P18 ?instanceof.
?instanceof ppt:P24* pp:Q2
}
?host ppt:P11 ?ncbi
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
BIND (ENCODE_FOR_URI(REPLACE(STR(?host), ".*Q", "Q")) AS ?qid) # article item
BIND ("Q2" AS ?P18)
}
Generate QuickStatements to add "instance of: placeholder taxon" to items with P28 statements
P28 "representative sequence for placeholder taxon" is intended for placeholder taxa, i.e. items that are described in the literature like taxa or provisional taxa and have a published phylogenetic marker sequence, but where a matching taxon ID in NCBI Taxonomy is not yet assigned.
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
PREFIX pps: <https://ppsdb.wikibase.cloud/prop/>
PREFIX ppss: <https://ppsdb.wikibase.cloud/prop/statement/>
PREFIX ppsq: <https://ppsdb.wikibase.cloud/prop/qualifier/>
SELECT DISTINCT ?qid ?P18 WHERE {
?item ppt:P28 ?repseq
FILTER NOT EXISTS {
?item ppt:P18 pp:Q56
}
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
BIND (ENCODE_FOR_URI(REPLACE(STR(?item), ".*Q", "Q")) AS ?qid) # article item
BIND ("Q56" AS ?P18)
}
List all classes
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?class ?classLabel WHERE {
?item ppt:P18 ?class
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
Taxon items without parent taxon
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?item ?qid ?itemLabel WHERE {
?item ppt:P18 pp:Q2.
FILTER NOT EXISTS {
?item ppt:P29 ?parent.
}
BIND (ENCODE_FOR_URI(REPLACE(STR(?item), ".*Q", "Q")) AS ?qid)
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
Items that are in a maintenance class
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT DISTINCT ?item ?itemLabel ?classLabel WHERE {
?item ppt:P18 ?class.
?class ppt:P24* pp:Q657
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
Statistics
Count interactions per host taxon, report in descending order
Treat these counts with a pinch of salt, because species concepts differ.
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT ?host ?hostLabel (COUNT (DISTINCT ?symbiont) AS ?count) WHERE {
?host ppt:P19 ?symbiont.
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
} GROUP BY ?host ?hostLabel ORDER BY DESC(?count)
Count interactions per symbiont taxon, report in descending order
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
SELECT ?symbiont ?symbiontLabel (COUNT (DISTINCT ?host) AS ?count) WHERE {
?host ppt:P19 ?symbiont.
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
} GROUP BY ?symbiont ?symbiontLabel ORDER BY DESC(?count)