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ontologypath.txt
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ontologypath.txt
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import rdflib
from SPARQLWrapper import SPARQLWrapper, JSON
from rdflib import Graph, URIRef, Literal, Namespace, RDF
import re
import timeit
import time
def NCIone(c1,c2,rel):
c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
final={}
re1=" SELECT ?pred1 WHERE {<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c1+"> ?pred1 "
re2=" <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c2+">} "
path=""
res_new=re1+re2
print(res_new)
query_mesh=str(res_new)
#print(reason)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
print(prop1,row["obj"])
#prop2=row["pred2"].rsplit('/', 1)[-1]
#prop3=row["pred3"].rsplit('/', 1)[-1]
#final="Entity:"+c1+c2+"s:"+row["pred1"]+"pred:"+row["pred2"]
path=str(prop1)
return path
def NCItwo(c1,c2,rel):
c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
final={}
re1=" SELECT ?pred1 ?b ?pred2 WHERE {<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c1+"> ?pred1 ?b. ?b ?pred2 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c2+">} "
path=""
res_new=re1
print(res_new)
query_mesh=str(res_new)
#print(reason)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
#final="Entity:"+c1+c2+"s:"+row["pred1"]+"pred:"+row["pred2"]
path=str(prop1)+str(prop2)+str(prop3)
return path
def NCIthree(c1,c2,rel):
c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
final={}
re1=" SELECT ?pred1 ?b ?pred2 ?c ?pred3 WHERE {<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c1+"> ?pred1 ?b. ?b ?pred2 ?c. ?c ?pred3 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c2+">} "
path=""
res_new=re1
print(res_new)
query_mesh=str(res_new)
#print(reason)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
prop4=row["c"].rsplit('/', 1)[-1]
prop5=row["pred3"].rsplit('/', 1)[-1]
#final="Entity:"+c1+c2+"s:"+row["pred1"]+"pred:"+row["pred2"]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)
return path
def NCIaxiom1(c1,c2,g1):
query="Select ?pred1 ?b ?d ?e ?f where{{?a ?pred1 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c1+">} {?a ?b _:c} { _:c ?d ?e} {?e ?f <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c2+"> } }"
print(query)
result=g1.query(query)
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["d"].rsplit('/', 1)[-1]
prop4=row["e"].rsplit('/', 1)[-1]
prop5=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)
return path
def NCIaxiom2(c1,c2,g1):
query="Select ?pred1 ?a ?b ?d ?e ?f ?g where{ {?a ?pred1 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c1+">} {?a ?b _:c} { _:c ?d ?e} {?e ?f ?g} {?g ?h <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"+c2+"> } }"
print(query)
result=g1.query(query)
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["a"].rsplit('/', 1)[-1]
prop3=row["b"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["e"].rsplit('/', 1)[-1]
prop6=row["f"].rsplit('/', 1)[-1]
prop7=row["g"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)+str(prop6)+str(prop7)
return path
def convert(prop):
#print(prop)
prop=prop.replace("AQ","actual outcome")
prop=prop.replace("QB","has actual outcome")
prop=prop.replace("RQ","classifies")
prop=prop.replace("RO","measures")
prop=prop.replace("SY","same as")
prop=prop.replace("CHD","is a ,part of")
prop=prop.replace("PAR","inverse is a ,has part")
prop=prop.replace("SIB", "sibling is in a")
prop=prop.replace("RN","tradename of")
prop=prop.replace("RB","has tradesname")
return prop
def medline_direct(c1,c2,g1):
start_time = timeit.default_timer()
res_direct= """
PREFIX MEDLINE: <http://purl.bioontology.org/ontology/MEDLINEPLUS/>
SELECT DISTINCT ?pred1
WHERE { MEDLINE:"""+c1+""" ?pred1 MEDLINE:"""+c2+""" .
}"""
prop1=""
direct_res=g1.query(res_direct)
for row in direct_res:
prop1=row["pred1"].rsplit('/', 1)[-1]
print("direct")
print(timeit.default_timer() - start_time)
return convert(prop1)
def medline_hop1(c1,c2,g1):
start_time = timeit.default_timer()
res_medline = """
PREFIX MEDLINE: <http://purl.bioontology.org/ontology/MEDLINEPLUS/>
SELECT DISTINCT ?pred1 ?c ?pred2
WHERE { MEDLINE:"""+c1+""" ?pred1 ?c. ?c ?pred2 MEDLINE:"""+c2+""" .
}"""
prop1=""
res_med = g1.query(res_medline)
for row in res_med:
#print(f"{row.pred1} {row.c} {row.pred2}")
pred1=row["pred1"].rsplit('/', 1)[-1]
c=row["c"].rsplit('/', 1)[-1]
pred2=row["pred2"].rsplit('/', 1)[-1]
#final="Entity1: "+head+"Entity2: "+tail+"Actual relation: "+rel+"predicate1: "+row["pred1"]+"predicate2: "+row["pred2"]
prop1=str(convert(pred1))+" "+str(medline_label(c))+" "+str(convert(pred2))
print(timeit.default_timer() - start_time, "hop1 seconds")
return prop1
def medline_label(c1):
query="SELECT ?o where{ <http://purl.bioontology.org/ontology/MEDLINEPLUS/"+c1+"> <http://www.w3.org/2004/02/skos/core#prefLabel> ?o}"
queryres=g1.query(query)
for row in queryres:
return row["o"]
def medline_hop2(c1,c2,g1):
start_time = timeit.default_timer()
res_medline = """
PREFIX MEDLINE: <http://purl.bioontology.org/ontology/MEDLINEPLUS/>
SELECT DISTINCT ?pred1 ?c ?pred2 ?d ?pred3
WHERE { MEDLINE:"""+c1+""" ?pred1 ?c. ?c ?pred2 ?d. ?d ?pred3 MEDLINE:"""+c2+""" .
}"""
res_med = g1.query(res_medline)
path=""
for row in res_med:
path=""
#print(f"{row.pred1} {row.c} {row.pred2}")
#query="SELECT ?o where{ <http://purl.bioontology.org/ontology/MEDLINEPLUS/"+c1+"> <http://www.w3.org/2004/02/skos/core#prefLabel> ?o}"
#queryres=g1.query(query)
#for row1 in queryres:
# print(row1["o"])
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["c"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["pred3"].rsplit('/', 1)[-1]
path=(str(convert(prop1))+" "+str(medline_label(prop2))+" "+str(convert(prop3))+" "+str(medline_label(prop4))+" "+str(convert(prop5)))
print(timeit.default_timer() - start_time, "hop2 seconds")
return path
def medline_hop3(c1,c2,g1):
start_time = timeit.default_timer()
res_medline = """
PREFIX MEDLINE: <http://purl.bioontology.org/ontology/MEDLINEPLUS/>
SELECT DISTINCT ?pred1 ?c ?pred2 ?d ?pred3 ?e ?pred4
WHERE { MEDLINE:"""+c1+""" ?pred1 ?c. ?c ?pred2 ?d. ?d ?pred3 ?e. ?e ?pred4 MEDLINE:"""+c2+""" .
}"""
res_med = g1.query(res_medline)
path=""
for row in res_med:
path=""
#print(f"{row.pred1} {row.c} {row.pred2}")
#query="SELECT ?o where{ <http://purl.bioontology.org/ontology/MEDLINEPLUS/"+c1+"> <http://www.w3.org/2004/02/skos/core#prefLabel> ?o}"
#queryres=g1.query(query)
#for row1 in queryres:
# print(row1["o"])
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["c"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["pred3"].rsplit('/', 1)[-1]
prop6=row["e"].rsplit('/', 1)[-1]
prop7=row["pred4"].rsplit('/', 1)[-1]
path=(str(convert(prop1))+" "+str(medline_label(prop2))+" "+str(convert(prop3))+" "+str(medline_label(prop4))+" "+str(convert(prop5))+" "+str(medline_label(prop6))+" "+str(convert(prop7)))
print("hop3 :",timeit.default_timer() - start_time, "hop3 seconds")
return path
def medline_axiom1(c1,c2,g1):
start_time = timeit.default_timer()
res_medline = """
PREFIX MEDLINE: <http://purl.bioontology.org/ontology/MEDLINEPLUS/>
SELECT DISTINCT ?pred1 ?a ?b ?d ?e ?pred4
WHERE {{ MEDLINE:"""+c1+""" ?pred1 ?a} {?a ?b _:c} { _:c ?d ?e} {?e ?pred4 MEDLINE:"""+c2+ "}}"
res_med = g1.query(res_medline)
path=""
for row in res_med:
path=""
#print(f"{row.pred1} {row.c} {row.pred2}")
#query="SELECT ?o where{ <http://purl.bioontology.org/ontology/MEDLINEPLUS/"+c1+"> <http://www.w3.org/2004/02/skos/core#prefLabel> ?o}"
#queryres=g1.query(query)
#for row1 in queryres:
# print(row1["o"])
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["a"].rsplit('/', 1)[-1]
prop3=row["b"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["e"].rsplit('/', 1)[-1]
prop6=row["pred4"].rsplit('/', 1)[-1]
path=(str(convert(prop1))+" "+str(medline_label(prop2))+" "+str(convert(prop3))+" "+str(convert(prop4))+" "+str(medline_label(prop5))+" "+str(convert(prop6)))
print(timeit.default_timer() - start_time, "axiom1 seconds")
return path
def medline_axiom2(c1,c2,g1):
start_time = timeit.default_timer()
res_medline = """
PREFIX MEDLINE: <http://purl.bioontology.org/ontology/MEDLINEPLUS/>
SELECT DISTINCT ?pred1 ?a ?b ?d ?g ?pred4
WHERE {{ MEDLINE:"""+c1+""" ?pred1 ?a} {?a ?b _:c} { _:c ?d ?e} {?e ?f ?g }{?g ?pred4 MEDLINE:"""+c2+ "}}"
res_med = g1.query(res_medline)
path=""
for row in res_med:
path=""
#print(f"{row.pred1} {row.c} {row.pred2}")
#query="SELECT ?o where{ <http://purl.bioontology.org/ontology/MEDLINEPLUS/"+c1+"> <http://www.w3.org/2004/02/skos/core#prefLabel> ?o}"
#queryres=g1.query(query)
#for row1 in queryres:
# print(row1["o"])
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["a"].rsplit('/', 1)[-1]
prop3=row["b"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["e"].rsplit('/', 1)[-1]
prop6=row["f"].rsplit('/', 1)[-1]
prop7=row["g"].rsplit('/', 1)[-1]
prop8=row["pred4"].rsplit('/', 1)[-1]
path=(str(convert(prop1))+" "+str(medline_label(prop2))+" "+str(convert(prop3))+" "+str(convert(prop4))+" "+str(medline_label(prop5))+" "+str(convert(prop6))+str(medline_label(prop7))+str(convert(prop8)))
print(timeit.default_timer() - start_time, "axiom2 seconds")
return path
def NDFRTone(c1,c2,g1):
c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
final={}
re1= "SELECT ?pred WHERE {?s <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re2="'"
re3= c1
re4="'"
re5= "^^xsd:string."
re6= "?s ?pred ?b."
re7="?b <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re8="'"
re9=c2
re10="'"
re11="^^xsd:string."
re12="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10+re11+re12
path=""
print(res_new)
query_mesh=str(res_new)
#print(reason)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred"].rsplit('/', 1)[-1]
print(prop1)
path=str(prop1)
return path
def NDFRTtwo(c1,c2,g1):
c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
final={}
re1= "SELECT ?pred1 ?b ?pred2 ?c WHERE {?s <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re2="'"
re3= c1
re4="'"
re5= "^^xsd:string."
re6= "?s ?pred1 ?b. ?b ?pred2 ?c. "
re7="?c <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re8="'"
re9=c2
re10="'"
re11="^^xsd:string."
re12="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10+re11+re12
path=""
print(res_new)
query_mesh=str(res_new)
#print(reason)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
prop4=row["c"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)
#path=str(prop1)
return path
def NDFRTthree(c1,c2,g1):
c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
final={}
re1= "SELECT ?pred1 ?b ?pred2 ?c ?pred3 ?d WHERE {?s <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re2="'"
re3= c1
re4="'"
re5= "^^xsd:string."
re6= "?s ?pred1 ?b. ?b ?pred2 ?c. ?c ?pred3 ?d."
re7="?d <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re8="'"
re9=c2
re10="'"
re11="^^xsd:string."
re12="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10+re11+re12
path=""
print(res_new)
query_mesh=str(res_new)
#print(reason)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
prop4=row["c"].rsplit('/', 1)[-1]
prop5=row["pred3"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)+str(prop6)
#path=str(prop1)
return path
def NDFRTaxiom1(c1,c2,g1):
re1= "SELECT ?pred1 ?b ?pred2 ?c ?pred3 ?d WHERE {?a <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re2="'"
re3= c1
re4="'"
re5= "^^xsd:string."
re6= "{?a ?b _:c} { _:c ?d ?e}"
re7="?e <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re8="'"
re9=c2
re10="'"
re11="^^xsd:string."
re12="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10+re11+re12
result=g1.query(res_new)
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["pred2"].rsplit('/', 1)[-1]
prop4=row["c"].rsplit('/', 1)[-1]
prop5=row["pred3"].rsplit('/', 1)[-1]
prop6=row["d"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)+str(prop6)
return path
def NDFRTaxiom2(c1,c2,g1):
re1= "SELECT ?b ?d ?e ?f ?g WHERE {?a <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re2="'"
re3= c1
re4="'"
re5= "^^xsd:string."
re6= "{?a ?b _:c} { _:c ?d ?e} {?e ?f ?g}"
re7="?g <http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#UMLS_CUI> "
re8="'"
re9=c2
re10="'"
re11="^^xsd:string."
re12="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10+re11+re12
result=g1.query(res_new)
path=""
for row in result:
if(len(row)>0):
prop1=row["b"].rsplit('/', 1)[-1]
prop2=row["d"].rsplit('/', 1)[-1]
prop3=row["e"].rsplit('/', 1)[-1]
prop4=row["f"].rsplit('/', 1)[-1]
prop5=row["g"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)
return path
def dinto_one(c1,c2,g2):
#c1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
#c2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
startTime = time.time()
path=""
sub1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
sub2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
re5="SELECT ?x1 ?pred1 ?x2 WHERE{{?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?x1 }"
re6= "{?s1 ?pred1 ?b}."
re7="{?b <http://www.w3.org/2000/01/rdf-schema#label> ?x2}"
re8=" FILTER(regex(str(?x1),"
re9='"'
re10= str(sub1)+'"'
re11=") && regex(str(?x2),"
re12='"'
re13=str(sub2)+'"'
re14="))}"
query_mesh=re5+re6+re7+re8+re9+re10+re11+re12+re13+re14
print(query_mesh)
#print(reason)
res_n = g2.query(query_mesh)
executionTime = (time.time() - startTime)
print('Execution time in dinto one seconds: ' + str(executionTime))
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
path=str(prop1)
return path
def dinto_two(c1,c2,g2):
startTime = time.time()
path=""
sub1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
sub2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
re5="SELECT ?x1 ?pred1 ?pred2 ?c WHERE{{?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?x1 }"
re6= "{?s1 ?pred1 ?b}. {?b ?pred2 ?c}"
re7="{?c <http://www.w3.org/2000/01/rdf-schema#label> ?x2}"
re8=" FILTER(regex(str(?x1),"
re9='"'
re10= str(sub1)+'"'
re11=") && regex(str(?x2),"
re12='"'
re13=str(sub2)+'"'
re14="))}"
query_mesh=re5+re6+re7+re8+re9+re10+re11+re12+re13+re14
print(query_mesh)
#print(reason)
res_n = g2.query(query_mesh)
executionTime = (time.time() - startTime)
print('Execution time in DINTO two seconds: ' + str(executionTime))
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["pred2"].rsplit('/',1)[-1]
path=str(prop1)+str(row["c"])+str(prop2)
return path
def dinto_three(c1,c2,g2):
startTime = time.time()
path=""
sub1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
sub2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
re5="SELECT ?pred1 ?pred2 ?pred3 ?c ?d ?x2 WHERE{{?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?x1 }"
re6= "{?s1 ?pred1 ?b}. {?b ?pred2 ?c} {?c ?pred3 ?d}"
re7="{?d <http://www.w3.org/2000/01/rdf-schema#label> ?x2}"
re8=" FILTER(regex(str(?x1),"
re9='"'
re10= str(sub1)+'"'
re11=") && regex(str(?x2),"
re12='"'
re13=str(sub2)+'"'
re14="))}"
query_mesh=re5+re6+re7+re8+re9+re10+re11+re12+re13+re14
#print(query_mesh)
res_n = g2.query(query_mesh)
executionTime = (time.time() - startTime)
print('Execution time in dinto three seconds: ' + str(executionTime))
prop1=""
prop2=""
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["pred2"].rsplit('/', 1)[-1]
prop3=row["pred3"].rsplit('/', 1)[-1]
path=str(prop1)+str(row["b"])+str(prop2)+str(row["c"])+str(prop3)+str(row["d"])
return path
def dinto_axiom1(c1,c2,g2):
startTime = time.time()
path=""
sub1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
sub2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
q1="Select ?pred1 ?b ?d ?f where{{?a ?pred1 ?all1}{?a ?b _:c} { _:c ?d ?e} {?e ?f ?g }"
q2="FILTER regex(?all1,'"
q3=sub1+"') FILTER regex(?g,'"+sub2+"')}"
query=q1+q2+q3
#print(query)
result=g1.query(query)
executionTime = (time.time() - startTime)
print('Execution time in dinto axiom1seconds: ' + str(executionTime))
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["d"].rsplit('/', 1)[-1]
prop4=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)
return path
def dinto_axiom2(c1,c2,g2):
startTime = time.time()
path=""
sub1 = re.sub(r'[^a-zA-Z0-9\s]', '', c1)
sub2 = re.sub(r'[^a-zA-Z0-9\s]', '', c2)
q1="Select ?pred1 ?pred2 ?b ?d ?f where{{?a ?pred1 ?all0}{?a ?pred2 ?all1}{?all1 ?b _:c} { _:c ?d ?e} {?e ?f ?g }"
q2="FILTER regex(?all1,'"
q3=sub1+"') FILTER regex(?g,'"+sub2+"')}"
query=q1+q2+q3
#print(query)
result=g1.query(query)
executionTime = (time.time() - startTime)
print('Execution time in dinto axiom2 seconds: ' + str(executionTime))
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["pred2"].rsplit('/', 1)[-1]
prop3=row["b"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)
return path
def oae_path1(c1,c2,g1):
path=""
q31="SELECT ?a ?b ?c ?d WHERE {{?a ?p "
q32='"'
q33=str(ent1)
q34='"'
q35="} {?a ?b ?c}{?c ?d "
q36='"'
q37=str(ent2)
q38='"}}'
res_new=q31+q32+q33+q34+q35+q36+q37+q38
query_mesh=str(res_new)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["d"].rsplit('/', 1)[-1]
path=str(row["a"])+str(prop2)+str(row["c"])+str(prop3)
return path
def oae_path2(c1,c2,g1):
path=""
q31="SELECT ?a ?b ?c ?d ?e ?f WHERE {{?a ?p "
q32='"'
q33=str(ent1)
q34='"'
q35="} {?a ?b ?c} {?c ?d ?e}{?e ?f "
q36='"'
q37=str(ent2)
q38='"}}'
res_new=q31+q32+q33+q34+q35+q36+q37+q38
query_mesh=str(res_new)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["b"].rsplit('/', 1)[-1]
prop2=row["d"].rsplit('/', 1)[-1]
path=str(row["a"])+str(prop1)+str(row["c"])+str(prop2)+str(row["e"])
return path
def oae_path3(c1,c2,g1):
path=""
q31="SELECT ?b ?c ?d ?e ?f ?g ?h WHERE {{?a ?p "
q32='"'
q33=str(ent1)
q34='"'
q35="} {?a ?b ?c} {?c ?d ?e} {?e ?f ?g}{?g ?h "
q36='"'
q37=str(ent2)
q38='"}}'
res_new=q31+q32+q33+q34+q35+q36+q37+q38
query_mesh=str(res_new)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["b"].rsplit('/', 1)[-1]
prop2=row["d"].rsplit('/', 1)[-1]
prop3=row["f"].rsplit('/', 1)[-1]
path=str(row["a"])+str(prop1)+str(row["c"])+str(prop2)+str(row["e"])+str(prop3)
return path
def oae_axiom1(c1,c2,g1):
path=""
q31="SELECT ?b ?d ?e ?f WHERE {{?a ?p "
q32='"'
q33=str(ent1)
q34='"'
q35="} {?a ?b _:c} { _:c ?d ?e} {?e ?f "
q36='"'
q37=str(ent2)
q38='"}}'
res_new=q31+q32+q33+q34+q35+q36+q37+q38
query_mesh=str(res_new)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["b"].rsplit('/', 1)[-1]
prop2=row["d"].rsplit('/', 1)[-1]
prop3=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(row["e"])+str(prop3)
return path
def oae_axiom2(c1,c2,g1):
path=""
q31="SELECT ?b ?d ?e ?f ?g ?h WHERE {{?a ?p "
q32='"'
q33=str(ent1)
q34='"'
q35="} {?a ?b _:c} { _:c ?d ?e} {?e ?f ?g}{?g ?h "
q36='"'
q37=str(ent2)
q38='"}}'
res_new=q31+q32+q33+q34+q35+q36+q37+q38
query_mesh=str(res_new)
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["b"].rsplit('/', 1)[-1]
prop2=row["d"].rsplit('/', 1)[-1]
prop3=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(row["e"])+str(prop3)+str(row["g"])
return path
def path(ontologyname,c1,c2,g1):
path1=""
path2=""
path3=""
pathaxiom1=""
pathaxiom2=""
# For Biorel dataset chose from MEDLINE, NCI, NDFRT
# For ADE dataset chose from DINTO, OAE and DRON ontology
if(ontologyname=="MEDLINE"):
path1=medline_direct(c1,c2,g1)
path2=medline_hop1(c1,c2,g1)
path3=medline_hop2(c1,c2,g1)
pathaxiom1=medline_axiom1(c1,c2,g1)
pathaxiom2=medline_axiom2(c1,c2,g1)
elif(ontologyname=="NCI"):
path1=NCIone(c1,c2,g1)
path2=NCItwo(c1,c2,g1)
path3=NCIthree(c1,c2,g1)
pathaxiom1=NCIaxiom1(c1,c2,g1)
pathaxiom2=NCIaxiom2(c1,c2,g1)
elif(ontologyname=="NDFRT"):
path1=NDFRTone(c1,r2,g1)
path2=NDFRTtwo(c1,c2,g1)
path3=NDFRTthree(c1,c2,g1)
pathaxiom1=NDFRTaxiom1(c1,c2,g1)
pathaxiom2=NDFRTaxiom2(c1,c2,g1)
elif(ontologyname=="DINTO"):
path1=dinto_one(c1,c2,g1)
path2=dinto_two(c1,c2,g1)
path3=dinto_three(c1,c2,g1)
pathaxiom1=dinto_axiom1(c1,c2,g1)
pathaxiom2=dinto_axiom2(c1,c2,g1)
elif(ontologyname=="OAE"):
path1=oae_path1(c1,c2,g1)
path2=oae_path2(c1,c2,g1)
path3=oae_path3(c1,c2,g1)
pathaxiom1=oae_axiom1(c1,c2,g1)
pathaxiom2=oae_axiom2(c1,c2,g1)
else:
print("please enter correct ontology")
return path1,path2,path3,pathaxiom1,pathaxiom2
def triplets(c1,c2,g1):
query="SELECT ?s ?p ?o WHERE {?s ?p ?o}"
result=g1.query(query)
for res in result:
print(res["s"],res["p"],res["o"])
ontologyname="DINTO"
if(ontologyname=="MEDLINE"):
g1 = rdflib.Graph()
g1.parse('./ontology/MEDLINEPLUS.ttl', format='ttl')
elif(ontologyname=="NCI"):
g1 = rdflib.Graph()
g1.parse("./ontology/NCI.owl")
elif(ontologyname=="NDFRT"):
g1=rdflib.Graph()
g1.parse("./ontology/NDF-RT.owl")
elif(ontologyname=="OAE"):
g1 = rdflib.Graph()
g1 = g1.parse('./ontology/oae_merged.owl')
elif(ontologyname=="DINTO"):
g1=rdflib.Graph()
g1=g1.parse('./ontology/owlapi.xrdf',format="xml")
"""
with open("entpair.txt") as f:
file =f.readlines()
for line in file:
fullline=line.split(",")
for line in fullline:
lst = line.strip(" ").split("|")
if(len(lst))>0:
number1 = re.sub(r'[^a-zA-Z0-9\s]', '', lst[0])
number2 = re.sub(r'[^a-zA-Z0-9\s]', '', lst[1])
print(number1,number2)
NCIone(number1,number2,"")
#path1,path2,path3,pathaxiom1,pathaxiom2=path(ontologyname,"C0023819","C1333460",g1)
#final=str(path1)+"|"+str(path2)+"|"+str(path3)+"|"+str(pathaxiom1)+"|"+str(pathaxiom2)
#print("path1:",path1,"path2:",path2,"path3:",path3,"pathaxiom1",pathaxiom1,"pathaxiom2",pathaxiom2)
for line in open("./data/ADE-Corpus-V2/ADE.txt").read().split('\n'):
if(len(line))>0:
lst = line.split('|')
#entity.append(lst[2])
#entity.append(lst[5])
path1=""
path2=""
path3=""
pathaxiom1=""
pathaxiom2=""
path1,path2,path3,pathaxiom1,pathaxiom2=path(ontologyname,lst[2],lst[5],g1)
final=str(path1)+"|"+str(path2)+"|"+str(path3)+"|"+str(pathaxiom1)+"|"+str(pathaxiom2)
print("path1:",path1,"path2:",path2,"path3:",path3,"pathaxiom1",pathaxiom1,"pathaxiom2",pathaxiom2)
"""
def two(c1,c2,rel):
re1= " SELECT ?pred1 ?pred2 ?pred3 ?pred4 WHERE {?a ?pred1 "
re2="'"
re3= c1
re4="'"
re5= "?a ?pred2 ?b. ?b ?pred3 ?c."
re6="?c ?pred4 "
re7="'"
re8=c2
re9="'"
re10="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10
query_mesh=str(res_new)
res_n = g1.query(query_mesh)
path=""
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["pred2"].rsplit('/', 1)[-1]
prop3=row["pred3"].rsplit('/', 1)[-1]
prop4=row["pred4"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)
return path
def three(c1,c2,rel):
re1= " SELECT ?pred1 ?pred2 ?pred3 ?pred4 ?pred5 WHERE {?a ?pred1 "
re2="'"
re3= c1
re4="'"
re5= "?a ?pred2 ?b. ?b ?pred3 ?c. ?d ?pred4 ?e"
re6="?e ?pred5 "
re7="'"
re8=c2
re9="'"
re10="}"
res_new=re1+re2+re3+re4+re5+re6+re7+re8+re9+re10
query_mesh=str(res_new)
path=""
res_n = g1.query(query_mesh)
for row in res_n:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["pred2"].rsplit('/', 1)[-1]
prop3=row["pred3"].rsplit('/', 1)[-1]
prop4=row["pred4"].rsplit('/', 1)[-1]
prop5=row["pred5"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)
return path
def axiom1(c1,c2,rel):
q1="Select ?pred1 ?b ?d ?f where{{?a ?pred1 ?all1}{?a ?b _:c} { _:c ?d ?e} {?e ?f ?g }"
q2="FILTER regex(?all1,'"
q3=c1+"') FILTER regex(?g,'"+c2+"')}"
query=q1+q2+q3
print(query)
result=g1.query(query)
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["b"].rsplit('/', 1)[-1]
prop3=row["d"].rsplit('/', 1)[-1]
prop4=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)
return path
def axiom2(c1,c2,rel):
q1="Select ?pred1 ?pred2 ?b ?d ?f where{{?a ?pred1 ?all0}{?a ?pred2 ?all1}{?all1 ?b _:c} { _:c ?d ?e} {?e ?f ?g }"
q2="FILTER regex(?all1,'"
q3=c1+"') FILTER regex(?g,'"+c2+"')}"
query=q1+q2+q3
print(query)
result=g1.query(query)
path=""
for row in result:
if(len(row)>0):
prop1=row["pred1"].rsplit('/', 1)[-1]
prop2=row["pred2"].rsplit('/', 1)[-1]
prop3=row["b"].rsplit('/', 1)[-1]
prop4=row["d"].rsplit('/', 1)[-1]
prop5=row["f"].rsplit('/', 1)[-1]
path=str(prop1)+str(prop2)+str(prop3)+str(prop4)+str(prop5)
return path