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take into account MRREL concepts in different datasources #42

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take into account MRREL concepts in different datasources #42

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3 changes: 3 additions & 0 deletions conf_sample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,3 +14,6 @@

# Include the semantic type concepts for each Ontology file generated
INCLUDE_SEMANTIC_TYPES = True

# Remove duplication of triples when loading on cuis
LOAD_CUIS_REMOVE_DUPLICATION = True
55 changes: 42 additions & 13 deletions umls2rdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ def count(self):
cursor.close()
return int(record[0])

def scan(self,filt=None,limit=None):
def scan(self,filt=None,limit=None,inner_join=None):
#c = self.count()
i = 0
page = 0
Expand All @@ -207,9 +207,16 @@ def scan(self,filt=None,limit=None):
if self.load_select:
q = self.load_select
else:
q = "SELECT * FROM %s WHERE %s LIMIT %s OFFSET %s"%(self.table_name,filt,self.page_size,page * self.page_size)
if filt == None or len(filt) == 0:
q = "SELECT * FROM %s LIMIT %s OFFSET %s"%(self.table_name,self.page_size,page * self.page_size)
if inner_join:
if filt == None or len(filt) == 0:
q = "SELECT %s.* FROM %s %s LIMIT %s OFFSET %s"%(self.table_name,self.table_name,inner_join,self.page_size,page * self.page_size)
else:
q = "SELECT %s.* FROM %s %s WHERE %s LIMIT %s OFFSET %s" % (self.table_name, self.table_name, inner_join, filt, self.page_size, page * self.page_size)
else:
if filt == None or len(filt) == 0:
q = "SELECT * FROM %s LIMIT %s OFFSET %s" % (self.table_name, self.page_size, page * self.page_size)
else:
q = "SELECT * FROM %s WHERE %s LIMIT %s OFFSET %s" % (self.table_name, filt, self.page_size, page * self.page_size)
sys.stdout.write("[UMLS-Query] %s\n" % q)
sys.stdout.flush()
cursor.execute(q)
Expand Down Expand Up @@ -250,6 +257,7 @@ def __init__(self,ns,atoms=None,rels=None,
self.load_on_cuis = load_on_cuis
self.is_root = is_root
self.class_properties = dict()
self.loaded_triples = dict()

def code(self):
codes = set([get_code(x,self.load_on_cuis) for x in self.atoms])
Expand Down Expand Up @@ -361,15 +369,28 @@ def toRDF(self,fmt="Turtle",hierarchy=True,lang="en",tree=None):
#skip bogus HL7V3.0 root concept
continue
if not tree:
rdf_term += "\trdfs:subClassOf <%s> ;\n" % (o,)
# Use the option to remove duplications when loading by cuis
if conf.LOAD_CUIS_REMOVE_DUPLICATION:
triple = (url_term, "rdfs:subClassOf", o)
if not self.loaded_triples.has_key(triple):
rdf_term += "\trdfs:subClassOf <%s> ;\n" % (o,)
self.loaded_triples[triple] = True
else:
rdf_term += "\trdfs:subClassOf <%s> ;\n" % (o,)
else:
p = self.getURLTerm(get_rel_fragment(rel))
o = self.getURLTerm(target_code)
rdf_term += "\t<%s> <%s> ;\n" % (p,o)
# Use the option to remove duplications when loading by cuis
if conf.LOAD_CUIS_REMOVE_DUPLICATION:
triple = (url_term, p, o)
if not self.loaded_triples.has_key(triple):
rdf_term += "\t<%s> <%s> ;\n" % (p,o)
self.loaded_triples[triple] = True
else:
rdf_term += "\t<%s> <%s> ;\n" % (p, o)
if p not in self.class_properties:
self.class_properties[p] = \
UmlsAttribute(p,get_rel_fragment(rel))

for att in self.atts:
atn = att[MRSAT_ATN]
atv = att[MRSAT_ATV]
Expand All @@ -385,7 +406,7 @@ def toRDF(self,fmt="Turtle",hierarchy=True,lang="en",tree=None):
if len(atv.split(".")) == 1:
rdf_term += "\trdfs:subClassOf owl:Thing;\n"
p = self.getURLTerm(atn)
rdf_term += "\t<%s> \"\"\"%s\"\"\"^^xsd:string ;\n"%(p, escape(atv))
rdf_term += "\t<%s> \"\"\"%s\"\"\"^^xsd:string ;\n" % (p, escape(atv))
if p not in self.class_properties:
self.class_properties[p] = UmlsAttribute(p,atn)

Expand Down Expand Up @@ -484,9 +505,17 @@ def load_tables(self,limit=None):
mrsab = UmlsTable("MRSAB", self.con)
for sab_rec in mrsab.scan(filt="RSAB = '" + self.ont_code + "'", limit=1):
self.lang = sab_rec[MRSAB_LAT].lower()
mrconso_filt = "SAB = '%s' AND lat = '%s' AND SUPPRESS = 'N'"%(
self.ont_code,self.lang)
for atom in mrconso.scan(filt=mrconso_filt,limit=limit):

# In the case of loading by cuis, we can get more triples from the concepts that have relations in MRREL table but not in the same datasource in MRCONSO table
if self.load_on_cuis:
mrconso_filt = "lat = '%s' AND SUPPRESS = 'N'" % (self.lang)
mrconso_join = "INNER JOIN (SELECT CUI1 AS CUI FROM MRREL WHERE SAB = '%s' UNION SELECT CUI2 AS CUI FROM MRREL WHERE SAB = '%s') V1 ON MRCONSO.CUI = V1.CUI" % (
self.ont_code, self.ont_code)
else:
mrconso_filt = "SAB = '%s' AND lat = '%s' AND SUPPRESS = 'N'"%(self.ont_code,self.lang)
mrconso_join = None

for atom in mrconso.scan(filt=mrconso_filt,limit=limit,inner_join=mrconso_join):
index = len(self.atoms)
self.atoms_by_code[get_code(atom,self.load_on_cuis)].append(index)
if not self.load_on_cuis:
Expand Down Expand Up @@ -734,8 +763,8 @@ def write_semantic_types(self,sem_types,fout):
umls_code,alt_uri_code = umls_code.split(";")
if umls_code.startswith("#"):
continue
load_on_cuis = load_on_field == "load_on_cuis"
output_file = os.path.join(conf.OUTPUT_FOLDER,file_out)
load_on_cuis = load_on_field.strip() == "load_on_cuis"
output_file = os.path.join(conf.OUTPUT_FOLDER,file_out.strip())
sys.stdout.write("Generating %s (using '%s')\n" %
(umls_code,load_on_field))
sys.stdout.flush()
Expand Down