NXQ_00226

rq turtle/ttl

• dataset
• peptide
• proteomics
• tutorial

Proteins with at least 2 validating peptides >=9aa found in blood plasma, urine or cerebrospinal fluid (criteria for biomarker)].

Use at

• https://sparql.nextprot.org/sparql

PREFIX : <http://nextprot.org/rdf/>
PREFIX source: <http://nextprot.org/rdf/source/>

SELECT DISTINCT ?entry WHERE {
values ?pepsources {
 source:PeptideAtlas_human_Cerebrospinal_Fluid
 source:PeptideAtlas_human_Blood_Plasma
 source:PeptideAtlas_human_Urine
 source:MassIVE_human_Cerebrospinal_Fluid
 source:MassIVE_human_Blood_Plasma
 source:MassIVE_human_Urine
 }
 ?entry :isoform ?iso.
 ?iso :peptideMapping ?pm .
 ?pm :peptideName ?pepid .
 ?pm :evidence / :assignedBy ?pepsources .
 ?pm :proteotypic true .
 ?pm :start ?p1 ; :end ?p2 .
 filter(?p2-?p1 >= 8) # peptide length >= 9
}
group by ?entry having(count (distinct ?pepid) > 1) # at least two such peptides

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v8("?_anon_3b93fb9548914f3581febfeabf3844496020")
  v4("?entry"):::projected 
  v5("?iso")
  v2("?p1")
  v1("?p2")
  v7("?pepid")
  v3("?pepsources")
  v6("?pm")
  a2((" "))
  a1((" "))
  c9(["true^^xsd:boolean"]):::literal 
  f0[[" > '1^^xsd:integer'"]]
  f0 --> a1
  f1[["?p2 - ?p1 >= '8^^xsd:integer'"]]
  f1 --> v1
  f1 --> v2
  bind2[/VALUES ?pepsources/]
  bind2-->v3
  bind20([":source/PeptideAtlas_human_Cerebrospinal_Fluid"])
  bind20 --> bind2
  bind21([":source/PeptideAtlas_human_Blood_Plasma"])
  bind21 --> bind2
  bind22([":source/PeptideAtlas_human_Urine"])
  bind22 --> bind2
  bind23([":source/MassIVE_human_Cerebrospinal_Fluid"])
  bind23 --> bind2
  bind24([":source/MassIVE_human_Blood_Plasma"])
  bind24 --> bind2
  bind25([":source/MassIVE_human_Urine"])
  bind25 --> bind2
  v4 --":isoform"-->  v5
  v5 --":peptideMapping"-->  v6
  v6 --":peptideName"-->  v7
  v6 --":evidence"-->  a2
  a2 --":assignedBy"-->  v3
  v6 --":proteotypic"-->  c9
  v6 --":start"-->  v2
  v6 --":end"-->  v1
  bind4[/"count(?pepid)"/]
  v7 --o bind4
  bind4 --as--o v8