In [2]:
PC_Endpoint = \
"http://rdf.pathwaycommons.org/sparql"
We will use the sparqlwrapper library. Executing the sparql queries is straightforward (cf. the first four lines of runQuery(...) below), but we introduce some auxiliary functions for nicely displaying the results.
In [3]:
from SPARQLWrapper import SPARQLWrapper, JSON
from IPython.display import display, Markdown
# for telling jupyter to display the result as markdown
def runQuery(queryString, outputFormat="tsv", varList=[], truncateAt=30):
""" Send the query to the endpoint and attempt
to nicely display the result.
Possible values for outputFormat: "tsv", "markdown"
"""
sparql = SPARQLWrapper(PC_Endpoint)
sparql.setQuery(queryString)
sparql.setReturnFormat(JSON)
results = sparql.query().convert()
if outputFormat == "tsv":
displayQueryResultAsTSV(results, varList)
elif outputFormat == "markdown":
displayQueryResultAsMarkdown(results, varList, truncateAt)
def displayQueryResultAsTSV(queryResult, varList=[], truncateAt=30):
if len(queryResult["results"]["bindings"]) == 0:
print("Empty result")
return
if varList == []:
varList = [varName for varName in queryResult["results"]["bindings"][0].keys()]
displayResult = ""
for currentVar in varList:
displayResult += currentVar + "\t"
displayResult = displayResult[:-1] + "\n"
for result in queryResult["results"]["bindings"]:
for currentVar in varList:
if currentVar in result.keys():
displayResult += truncateString(result[currentVar]['value'], truncateAt) + "\t"
else:
displayResult += "\t"
displayResult = displayResult[:-1] + "\n"
print(displayResult)
def displayQueryResultAsMarkdown(queryResult, varList=[], truncateAt=30):
if len(queryResult["results"]["bindings"]) == 0:
print("Empty result")
return
if varList == []:
varList = [varName for varName in queryResult["results"]["bindings"][0].keys()]
displayResult = ""
sepLine = ""
for currentVar in varList:
displayResult += " | " + currentVar
sepLine += "| ---"
displayResult += "\n" + sepLine + "\n"
for result in queryResult["results"]["bindings"]:
for currentVar in varList:
if currentVar in result.keys():
displayResult += "| " + truncateString(result[currentVar]['value'], truncateAt) + " "
else:
displayResult += "| "
displayResult += " \n"
display(Markdown(displayResult))
def truncateString(message, length=30):
if (length == -1) or (len(message) <= length):
return message
return message[:15] + "..." + message[-12:]
For the sake of clarity, we will define the usual prefixes in the commonPrefixes variable.
In [17]:
commonPrefixes = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX bp3: <http://www.biopax.org/release/biopax-level3.owl#>
PREFIX taxon: <http://identifiers.org/taxonomy/>
PREFIX reactome: <http://identifiers.org/reactome/>
PREFIX release: <http://www.reactome.org/biopax/49/48887#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX uniprot: <http://purl.uniprot.org/uniprot/>
PREFIX bp: <http://www.biopax.org/release/biopax-level3.owl#>
PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX obo2: <http://purl.obolibrary.org/obo#>
"""
In [15]:
queryTFControllers = """
SELECT ?tempReac ?type ?controlledName ?controllerName ?source WHERE{
FILTER( (?controlledName = 'Transcription of SCN5A'^^<http://www.w3.org/2001/XMLSchema#string>)
and (?controllerName != 'SCN5A')
and (?source != 'mirtarbase') ) .
?tempReac a bp:TemplateReactionRegulation .
?tempReac bp:displayName ?reacName ;
bp:controlled ?controlled ;
bp:controller ?controller ;
bp:controlType ?type ;
bp:dataSource ?source .
?controlled bp:displayName ?controlledName .
?controller bp:displayName ?controllerName . }
GROUP BY ?controlledName ?controllerName
"""
runQuery(commonPrefixes + queryTFControllers, "markdown", [])
In [ ]: