Protist-Prokaryote Symbiosis Database

Project:SPARQL/examples

Revision as of 11:20, 20 March 2024 by Kbseah-wikibase (talk | contribs) (→‎Maintenance queries)

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 ?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". }
}

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Draw taxonomy tree from Euglenozoa

#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 ?parent ?parentLabel WHERE {
  ?host ppt:P29/ppt:P29* pp:Q775.
  ?host ppt:P29 ?parent.
  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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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)
}

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Generate QuickStatements to link interaction hosts to their genera

Split labels, e.g. "Paramecium caudatum" on whitespace, take the first word as a putative genus name, and look for items with taxon rank "genus" that match the putative genus name. Have to avoid assigning labels like "Cryptotermes symbiont", instead use "symbiont of Cryptotermes" to avoid false matches. 

PREFIX pp: <https://ppsdb.wikibase.cloud/entity/>
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bd: <http://www.bigdata.com/rdf#>
SELECT DISTINCT ?qid ?P29 WHERE {
  {
    SELECT DISTINCT ?item ?qid ?itemLabel ?maybeGenus WHERE {
      ?item ppt:P19 ?symbiont.
      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".
        ?item rdfs:label ?itemLabel.
      }
      BIND(STRBEFORE(?itemLabel, " ") AS ?maybeGenus)
    }
  }
  {
    SELECT DISTINCT ?item2 ?item2Label WHERE {
      ?item2 ppt:P32 pp:Q601;
        rdfs:label ?item2Label.
      FILTER((LANG(?item2Label)) = "en")
    }
  }
  FILTER(?item2Label = ?maybeGenus)
  BIND(ENCODE_FOR_URI(REPLACE(STR(?item), ".*Q", "Q")) AS ?qid)
  BIND(ENCODE_FOR_URI(REPLACE(STR(?item2), ".*Q", "Q")) AS ?P29)
}

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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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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". }
}

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DOIs used in reference qualifiers but not in a reference item

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 ?doi 
WITH {
  SELECT DISTINCT ?ref ?refdoi WHERE {
    ?ref ppt:P18 pp:Q3;
         ppt:P13 ?refdoi. 
  } 
} AS %refs
WHERE {
  INCLUDE %refs
  ?host pps:P19 ?interaction.
  ?interaction prov:wasDerivedFrom ?refnode.
  ?refnode ppsr:P27 ?doi.
  FILTER NOT EXISTS { ?refnode ppsr:P23 ?statedin }
  FILTER (?doi NOT IN (?refdoi))
}

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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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