neXtProt/NXQ_00276

Diseases/phenotypes associated with coding variants and associated publications for a given gene

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX db: <http://nextprot.org/rdf/db/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX so: <http://purl.obolibrary.org/obo/SO_>

SELECT DISTINCT ?entry (str(?umlsTerm) as ?umlsTermSTR) (str(?snpac) as ?varid) ?pos (str(?orgaa) as ?orgAA) (str(?varaa) as ?varAA) ?article WHERE {
 SERVICE <https://rdf.disgenet.org/sparql> {
 ?vda sio:SIO_000628 ?umls, ?variant .
 ?vda sio:SIO_000772 ?article .
 ?umls dcterms:title ?umlsTerm.
 {?umls a sio:SIO_010299 .} # disease
 union
 {?umls a sio:SIO_010056 .} # or phenotype
 ?variant a so:0001583 ; dcterms:title ?variantTitle . # Missense variant
 ?variant so:associated_with ?gene .
 ?gene a ncit:C16612; sio:SIO_010078 ?protein .
 ?gene sio:SIO_000205 ?gname.
 filter(contains(str(?gname),"HBB")) # Hemoglobin gene (NX_P68871)
 }

 BIND(IRI(replace(str(?protein),"purl","www")) AS ?unipage) .
 ?entry :swissprotPage ?unipage .
 ?entry :isoform ?iso .
 ?iso :swissprotDisplayed true .
 ?iso :variant ?var .
 ?var :evidence /:reference ?xref .
 ?xref :provenance db:dbSNP; :accession ?snpac .
 ?var :start ?pos ; :original ?orgaa; :variation ?varaa .
 filter(contains(?snpac,str(?variantTitle))) # matches the exact same variant Disgenet returned
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v7("?article"):::projected 
  v12("?entry"):::projected 
  v9("?gene")
  v3("?gname")
  v13("?iso")
  v21("?orgAA")
  v17("?orgaa"):::projected 
  v16("?pos"):::projected 
  v10("?protein")
  v1("?snpac"):::projected 
  v5("?umls")
  v8("?umlsTerm"):::projected 
  v19("?umlsTermSTR")
  v11("?unipage")
  v14("?var")
  v22("?varAA")
  v18("?varaa"):::projected 
  v6("?variant")
  v2("?variantTitle")
  v20("?varid")
  v4("?vda")
  v15("?xref")
  a1((" "))
  c7(["sio:SIO_010299"]):::iri 
  c8(["sio:SIO_010056"]):::iri 
  c22([":db/dbSNP"]):::iri 
  c9(["so:0001583"]):::iri 
  c11(["ncit:C16612"]):::iri 
  c17(["true^^xsd:boolean"]):::literal 
  f0[["contains(?snpac,str(?variantTitle))"]]
  f0 --> v1
  f0 --> v2
  subgraph s1["https://rdf.disgenet.org/sparql"]
    style s1 stroke-width:4px;
    f1[["contains(str(?gname),'HBB')"]]
    f1 --> v3
    v4 --"sio:SIO_000628"-->  v5
    v4 --"sio:SIO_000628"-->  v6
    v4 --"sio:SIO_000772"-->  v7
    v5 --"dcterms:title"-->  v8
    subgraph union0[" Union "]
    subgraph union0l[" "]
      style union0l fill:#abf,stroke-dasharray: 3 3;
      v5 --"a"-->  c8
    end
    subgraph union0r[" "]
      style union0r fill:#abf,stroke-dasharray: 3 3;
      v5 --"a"-->  c7
    end
    union0r <== or ==> union0l
    end
    v6 --"a"-->  c9
    v6 --"dcterms:title"-->  v2
    v6 --"so:associated_with"-->  v9
    v9 --"a"-->  c11
    v9 --"sio:SIO_010078"-->  v10
    v9 --"sio:SIO_000205"-->  v3
  end
  bind2[/"replace(str(?protein),'purl','www')"/]
  v10 --o bind2
  bind2 --as--o v11
  v12 --":swissprotPage"-->  v11
  v12 --":isoform"-->  v13
  v13 --":swissprotDisplayed"-->  c17
  v13 --":variant"-->  v14
  v14 --":evidence"-->  a1
  a1 --":reference"-->  v15
  v15 --":provenance"-->  c22
  v15 --":accession"-->  v1
  v14 --":start"-->  v16
  v14 --":original"-->  v17
  v14 --":variation"-->  v18
  bind3[/"str(?umlsTerm)"/]
  v8 --o bind3
  bind3 --as--o v19
  bind4[/"str(?snpac)"/]
  v1 --o bind4
  bind4 --as--o v20
  bind5[/"str(?orgaa)"/]
  v17 --o bind5
  bind5 --as--o v21
  bind6[/"str(?varaa)"/]
  v18 --o bind6
  bind6 --as--o v22