neXtProt/NXQ_00001

Proteins phosphorylated and located in the cytoplasm

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 ?cytoloc {nextprot_cv:SL-0086 nextprot_cv:GO_0005737} # SL and GO values for cytoplasm
 ?entry :isoform ?iso.
 ?iso :uniprotKeyword / :term nextprot_cv:KW-0597. # Phosphorylated
 ?iso :cellularComponent ?loc .
 ?loc :term /:childOf ?cytoloc.
 filter not exists {?loc :negativeEvidence ?negev} # No negative localization evidence
}

# Assign values to the variable ?cytoloc
# The values correspond to the two controlled vocabulary (cv) terms for cytoplam:
# SL-0086 is the UniProt subcellular location term
# GO_0005737 is the Gene Ontology cellular component term
#
# Use the same name of the variable (?iso and ?loc) in several statements.
# It is the name of the variable that enforces the constraints.
#
# Phosphorylated proteins are retrieved using a keyword:
# KW-0597 is the UniProt keyword for phosphorylated
#
# Use :childOf to include children of a term.
# Cytosol (SL-0091), the child term of cytoplasm, will thus be included.
#
# Exclude negative locatization evidences.
# This enforces that the protein is located in the cytoplasm.

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v3("?cytoloc")
  v4("?entry"):::projected 
  v5("?iso")
  v1("?loc")
  v2("?negev")
  a1((" "))
  a2((" "))
  c5([":terminology/KW-0597"]):::iri 
  f0[["not  "]]
  subgraph f0e0["Exists Clause"]
    e0v1 --":negativeEvidence"-->  e0v2
    e0v1("?loc"):::projected 
    e0v2("?negev"):::projected 
  end
  f0--EXISTS--> f0e0
  f0 --> v1
  f0 --> c1
  f0 --> v2
  v1 --":negativeEvidence"-->  v2
  bind1[/VALUES ?cytoloc/]
  bind1-->v3
  bind10([":terminology/SL-0086"])
  bind10 --> bind1
  bind11([":terminology/GO_0005737"])
  bind11 --> bind1
  v4 --":isoform"-->  v5
  v5 --":uniprotKeyword"-->  a1
  a1 --":term"-->  c5
  v5 --":cellularComponent"-->  v1
  v1 --":term"-->  a2
  a2 --":childOf"-->  v3