neXtProt/NXQ_00016

Proteins with a mature chain of less than 1000 amino acids which are secreted and do not contain cysteines in the mature chain

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX nextprot_cv: <http://nextprot.org/rdf/terminology/>

SELECT DISTINCT ?entry WHERE {
 values ?sloc {nextprot_cv:GO_0005576 nextprot_cv:SL-0243} # GO and SL values for secreted
 ?entry :isoform ?iso.
 ?iso :cellularComponent ?anno .
 ?anno :term /:childOf ?sloc .
 filter not exists { ?anno :negativeEvidence ?_ }
 #
 # filter not exists {?iso :cellularComponent /:term nextprot_cv:GO_0070062 .
 # filter not exists {?iso :cellularComponent /:term /:childOf nextprot_cv:SL-0243 .}
 # }
 # you can uncomment this to filters out extracellular exosome only location (2240 entries),
 # most of them evidenced only by large-scale proteomic analysis
 #
 ?iso :sequence / :chain ?seq.
 ?iso :matureProtein [ :start ?mstart ; :end ?mend]
 filter ((?mend-?mstart > 0) && (?mend-?mstart < 1000))
 bind (?mend - ?mstart + 1 as ?mlen)
 bind (substr(?seq, ?mstart, ?mlen) as ?mseq)
 filter (!regex (?mseq,'C'))
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v5("?_")
  v4("?anno")
  v7("?entry"):::projected 
  v8("?iso")
  v2("?mend")
  v10("?mlen")
  v11("?mseq")
  v3("?mstart")
  v9("?seq")
  v6("?sloc")
  a1((" "))
  a2((" "))
  a3((" "))
  f0[["not regex(?mseq,'C')"]]
  f0 --> v11
  f1[["?mend - ?mstart > '0^^xsd:integer'?mend - ?mstart < '1000^^xsd:integer'"]]
  f1 --> v2
  f1 --> v3
  f2[["not  "]]
  subgraph f2e0["Exists Clause"]
    e0v1 --":negativeEvidence"-->  e0v2
    e0v2("?_"):::projected 
    e0v1("?anno"):::projected 
  end
  f2--EXISTS--> f2e0
  f2 --> v4
  f2 --> c4
  f2 --> v5
  v4 --":negativeEvidence"-->  v5
  bind3[/VALUES ?sloc/]
  bind3-->v6
  bind30([":terminology/GO_0005576"])
  bind30 --> bind3
  bind31([":terminology/SL-0243"])
  bind31 --> bind3
  v7 --":isoform"-->  v8
  v8 --":cellularComponent"-->  v4
  v4 --":term"-->  a1
  a1 --":childOf"-->  v6
  v8 --":sequence"-->  a2
  a2 --":chain"-->  v9
  a3 --":start"-->  v3
  a3 --":end"-->  v2
  v8 --":matureProtein"-->  a3
  bind4[/"?mend - ?mstart + '1^^xsd:integer'"/]
  v2 --o bind4
  v3 --o bind4
  bind4 --as--o v10
  bind5[/"substring(?seq,?mstart,?mlen)"/]
  v9 --o bind5
  v3 --o bind5
  v10 --o bind5
  bind5 --as--o v11