Skip to main content

Examples​

We can then start asking some questions to the dataset. For instance, if we focus on kinases that are often overexpressed/mutated in various cancer subtypes:


'Which compounds exhibit sub-micromolar IC50 activity against kinase targets such as SRC, BTK, MAPK1, ABL1, AKT1, and PIK3CA?'

SPARQL query
PREFIX ex: <http://example.org/schema/>
PREFIX chemblm: <https://identifiers.org/chembl.compound/>
PREFIX chemblt: <https://identifiers.org/chembl.target/>

SELECT DISTINCT ?compound ?target ?uniprot ?value ?type
WHERE {
  GRAPH <http://example.org/graph/chembl-kinase-slice> {
    ?activity a ex:Activity ;
              ex:ofCompound ?compound ;
              ex:onTarget ?target ;
              ex:value ?value ;
              ex:activityType ?type .

    ?target a ex:Protein ;
            ex:uniprotAcc ?uniprot .

    FILTER(?uniprot IN (
      "P12931",  # SRC
      "P06239",  # SRC-family
      "P42680",  # BTK
      "P28482",  # MAPK1
      "P00519",  # ABL1
      "P31749",  # AKT1
      "P42336"   # PIK3CA
    ))
    FILTER(?type = "IC50")
    FILTER(xsd:double(?value) < 1000)
  }
}
LIMIT 10
Example 1

'Which ChEMBL kinase targets are expressed in normal kidney cortex with TPM > 1?'

SPARQL query
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX chemblt: <https://identifiers.org/chembl.target/>
PREFIX chemblm: <https://identifiers.org/chembl.compound/>
PREFIX ex: <http://example.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX sio: <http://semanticscience.org/resource/>

SELECT DISTINCT ?target ?uniprot ?ensembl ?sample ?tpm
WHERE {
  GRAPH <http://example.org/graph/chembl-kinase-slice> {
    ?target a ex:Protein ;
            ex:uniprotAcc ?uniprot .
  }
  BIND(IRI(CONCAT("http://purl.uniprot.org/uniprot/", ?uniprot)) AS ?uniprotIRI)

  GRAPH <http://example.org/graph/linkset-idmap> {
    ?uniprotIRI owl:sameAs ?ensembl .
  }
  GRAPH <http://example.org/graph/gtex-expr-v9> {
    ?expr sio:isAbout ?ensembl ;
          sio:isPartOf ?sample ;
          sio:has_value ?tpm ;
          sio:has_unit <http://purl.gtex/TPM> .

    ?sample sio:isAbout <http://purl.obolibrary.org/obo/UBERON_0002113>  # Kidney cortex
  }

  FILTER(xsd:float(?tpm) > 1)
}
ORDER BY DESC(xsd:float(?tpm))
LIMIT 10

Example 2