Project:SPARQL/examples

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". }
}

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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". }
}

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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". }
}

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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". }
}

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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". }
}

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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 ?target ?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 }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

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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)
}

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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". }
}

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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". }
}

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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)

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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)

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