neXtProt/NXQ_09630

Check there are no entries in the Cancer variants portal that do not have a variant phenotype annotation

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX cv: <http://nextprot.org/rdf/terminology/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

select distinct ?entry where {
  values ?gene
  {"APC" "ASXL1" "ATR" "BARD1" "BCOR" "BLM" "BMPR1A" "BRCA1" "BRCA2" "BRIP1"
  "CDH1" "CDKN1B" "DNMT3A" "EPCAM" "EZH2" "FLT3" "GATA1" "IDH1" "IDH2" "KIT"
  "KRAS" "MEN1" "MLH1" "MLH3" "MSH2" "MSH6" "MUTYH" "NF1" "NF2" "PALB2"
  "PIK3CA" "PMS2" "PRKAR1A" "RAD51C" "RAD51D" "RB1" "RUNX1" "SDHAF2" "SDHC" "SDHD"
  "SMAD4" "SMARCB1" "XRCC2"} # space-separated
  ?entry :gene / :name / rdfs:label ?genename .
  bind (str(?genename) as ?gn) # here we convert "xxx"^^xsd:string to "xxx" to match the values
  filter(?gn = ?gene)
  filter not exists {?entry :isoform /:proteoform /:phenotypicVariation ?phenotype} # No phenotype annotation
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?entry"):::projected 
  v5("?gene")
  v5("?genename")
  v6("?gn")
  v2("?phenotype")
  a3((" "))
  a4((" "))
  a1((" "))
  a2((" "))
  f0[["not  "]]
  subgraph f0e0["Exists Clause"]
    e0v1 --":isoform"-->  e0a1
    e0a1 --":proteoform"-->  e0a2
    e0a2 --":phenotypicVariation"-->  e0v2
    e0v1("?entry"):::projected 
    e0v2("?phenotype"):::projected 
    e0a1((" ")):::projected 
    e0a2((" ")):::projected 
  end
  f0--EXISTS--> f0e0
  f0 --> v1
  f0 --> c1
  f0 --> a1
  f0 --> c2
  f0 --> a2
  f0 --> c3
  f0 --> v2
  v1 --":isoform"-->  a1
  a1 --":proteoform"-->  a2
  a2 --":phenotypicVariation"-->  v2
  f1[["?gn = ?gene"]]
  f1 --> v6
  f1 --> v5
  bind2[/VALUES ?gene/]
  bind2-->v5
  bind20(["APC"])
  bind20 --> bind2
  bind21(["ASXL1"])
  bind21 --> bind2
  bind22(["ATR"])
  bind22 --> bind2
  bind23(["BARD1"])
  bind23 --> bind2
  bind24(["BCOR"])
  bind24 --> bind2
  bind25(["BLM"])
  bind25 --> bind2
  bind26(["BMPR1A"])
  bind26 --> bind2
  bind27(["BRCA1"])
  bind27 --> bind2
  bind28(["BRCA2"])
  bind28 --> bind2
  bind29(["BRIP1"])
  bind29 --> bind2
  bind210(["CDH1"])
  bind210 --> bind2
  bind211(["CDKN1B"])
  bind211 --> bind2
  bind212(["DNMT3A"])
  bind212 --> bind2
  bind213(["EPCAM"])
  bind213 --> bind2
  bind214(["EZH2"])
  bind214 --> bind2
  bind215(["FLT3"])
  bind215 --> bind2
  bind216(["GATA1"])
  bind216 --> bind2
  bind217(["IDH1"])
  bind217 --> bind2
  bind218(["IDH2"])
  bind218 --> bind2
  bind219(["KIT"])
  bind219 --> bind2
  bind220(["KRAS"])
  bind220 --> bind2
  bind221(["MEN1"])
  bind221 --> bind2
  bind222(["MLH1"])
  bind222 --> bind2
  bind223(["MLH3"])
  bind223 --> bind2
  bind224(["MSH2"])
  bind224 --> bind2
  bind225(["MSH6"])
  bind225 --> bind2
  bind226(["MUTYH"])
  bind226 --> bind2
  bind227(["NF1"])
  bind227 --> bind2
  bind228(["NF2"])
  bind228 --> bind2
  bind229(["PALB2"])
  bind229 --> bind2
  bind230(["PIK3CA"])
  bind230 --> bind2
  bind231(["PMS2"])
  bind231 --> bind2
  bind232(["PRKAR1A"])
  bind232 --> bind2
  bind233(["RAD51C"])
  bind233 --> bind2
  bind234(["RAD51D"])
  bind234 --> bind2
  bind235(["RB1"])
  bind235 --> bind2
  bind236(["RUNX1"])
  bind236 --> bind2
  bind237(["SDHAF2"])
  bind237 --> bind2
  bind238(["SDHC"])
  bind238 --> bind2
  bind239(["SDHD"])
  bind239 --> bind2
  bind240(["SMAD4"])
  bind240 --> bind2
  bind241(["SMARCB1"])
  bind241 --> bind2
  bind242(["XRCC2"])
  bind242 --> bind2
  v1 --":gene"-->  a3
  a3 --":name"-->  a4
  a4 --"rdfs:label"-->  v5
  bind3[/"str(?genename)"/]
  v5 --o bind3
  bind3 --as--o v6