def markNamedEntities(self, entityElements):
""" Marks tokens belonging to named entities
"""
namedEntityTokens = []
for entityElement in entityElements:
offsets = []
offsetStrings = entityElement.attrib["charOffset"].split(",")
for offsetString in offsetStrings:
charFrom, charTo = offsetString.split("-")
offset = (int(charFrom), int(charTo))
offsets.append(offset)
for k, v in self.tokensById.iteritems():
for offset in offsets:
if Range.overlap(offset, v.charOffset):
v.entities.append(entityElement.attrib["id"])
namedEntityTokens.append(v.id)
return namedEntityTokens
def markNamedEntities(self, entityElements):
""" Marks tokens belonging to named entities
"""
namedEntityTokens = []
for entityElement in entityElements:
offsets = []
offsetStrings = entityElement.attrib["charOffset"].split(",")
for offsetString in offsetStrings:
charFrom, charTo = offsetString.split("-")
offset = (int(charFrom), int(charTo))
offsets.append(offset)
for k,v in self.tokensById.iteritems():
for offset in offsets:
if Range.overlap(offset, v.charOffset):
v.entities.append(entityElement.attrib["id"])
namedEntityTokens.append(v.id)
return namedEntityTokens
def markBioInferInteractions(self, interactions):
""" Marks tokens belonging to a BioInfer interaction
"""
interactionTokens = []
for interaction in interactions:
offsets = []
offsetStrings = interaction[3].split(",")
for offsetString in offsetStrings:
charFrom, charTo = offsetString.split("-")
offset = (int(charFrom), int(charTo))
offsets.append(offset)
for k, v in self.tokensById.iteritems():
for offset in offsets:
if Range.overlap(offset, v.charOffset):
v.interactionWords.append(interaction[4])
interactionTokens.append(v.id)
return interactionTokens
def markBioInferInteractions(self, interactions):
""" Marks tokens belonging to a BioInfer interaction
"""
interactionTokens = []
for interaction in interactions:
offsets = []
offsetStrings = interaction[3].split(",")
for offsetString in offsetStrings:
charFrom, charTo = offsetString.split("-")
offset = (int(charFrom), int(charTo))
offsets.append(offset)
for k,v in self.tokensById.iteritems():
for offset in offsets:
if Range.overlap(offset, v.charOffset):
v.interactionWords.append(interaction[4])
interactionTokens.append(v.id)
return interactionTokens
