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 and interaction type

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 ?typeLabel ?symbiontLabel ?localizationLabel WHERE {
  ?host pps:P19 ?interaction.
  ?interaction ppss:P19 ?symbiont.
  OPTIONAL {
     ?interaction ppsq:P20 ?localization.
  }
  OPTIONAL {
     ?interaction ppsq:P26 ?type. 
  }
    
  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". }
}

Try it!