def main():
# Use file defined by BIOC_IN as default if no other provided
bioc_in = BIOC_IN
if len(sys.argv) >= 2:
bioc_in = sys.argv[1]
# A BioCReader object is put in place to hold the example BioC XML
# document
bioc_reader = BioCReader(bioc_in, dtd_valid_file=DTD_FILE)
# A BioCWRiter object is prepared to write out the annotated data
bioc_writer = BioCWriter(BIOC_OUT)
# The NLTK porter stemmer is used for stemming
stemmer = PorterStemmer()
# The example input file given above (by BIOC_IN) is fed into
# a BioCReader object; validation is done by the BioC DTD
bioc_reader.read()
# Pass over basic data
bioc_writer.collection = bioc_reader.collection
# Get documents to manipulate
documents = bioc_writer.collection.documents
# Go through each document
annotation_id = 0
for document in documents:
# Go through each passage of the document
for passage in document:
# Stem all the tokens found
stems = [
stemmer.stem(token)
for token in wordpunct_tokenize(passage.text)
]
# Add an anotation showing the stemmed version, in the
# given order
for stem in stems:
annotation_id += 1
# For each token an annotation is created, providing
# the surface form of a 'stemmed token'.
# (The annotations are collectively added following
# a document passage with a <text> tag.)
bioc_annotation = BioCAnnotation()
bioc_annotation.text = stem
bioc_annotation.id = str(annotation_id)
bioc_annotation.put_infon('surface form', 'stemmed token')
passage.add_annotation(bioc_annotation)
# Print file to screen w/o trailing newline
# (Can be redirected into a file, e. g output_bioc.xml)
sys.stdout.write(str(bioc_writer))
# Write to disk
bioc_writer.write()
def main():
# Use file defined by BIOC_IN as default if no other provided
bioc_in = BIOC_IN
if len(sys.argv) >= 2:
bioc_in = sys.argv[1]
# A BioCReader object is put in place to hold the example BioC XML
# document
bioc_reader = BioCReader(bioc_in, dtd_valid_file=DTD_FILE)
# A BioCWRiter object is prepared to write out the annotated data
bioc_writer = BioCWriter(BIOC_OUT)
# The NLTK porter stemmer is used for stemming
stemmer = PorterStemmer()
# The example input file given above (by BIOC_IN) is fed into
# a BioCReader object; validation is done by the BioC DTD
bioc_reader.read()
# Pass over basic data
bioc_writer.collection = bioc_reader.collection
# Get documents to manipulate
documents = bioc_writer.collection.documents
# Go through each document
annotation_id = 0
for document in documents:
# Go through each passage of the document
for passage in document:
# Stem all the tokens found
stems = [stemmer.stem(token) for
token in wordpunct_tokenize(passage.text)]
# Add an anotation showing the stemmed version, in the
# given order
for stem in stems:
annotation_id += 1
# For each token an annotation is created, providing
# the surface form of a 'stemmed token'.
# (The annotations are collectively added following
# a document passage with a <text> tag.)
bioc_annotation = BioCAnnotation()
bioc_annotation.text = stem
bioc_annotation.id = str(annotation_id)
bioc_annotation.put_infon('surface form',
'stemmed token')
passage.add_annotation(bioc_annotation)
# Print file to screen w/o trailing newline
# (Can be redirected into a file, e. g output_bioc.xml)
sys.stdout.write(str(bioc_writer))
# Write to disk
bioc_writer.write()
def add_annotation(triple, annotation_id):
# initialize annotation element
bioc_annotation = BioCAnnotation()
# MeSH term in a tag <text> ... </text> (origininal term, searched case insensitive)
bioc_annotation.text = triple[2]
# generate XML structure for the annotation and add infon
bioc_annotation.id = str(annotation_id)
bioc_annotation.put_infon('type', 'MeSH term')
# add location element
bioc_location = BioCLocation()
# add length of MeSH term
bioc_location.length = str(triple[1])
# add start position (offset)
bioc_location.offset = str(triple[0])
bioc_annotation.add_location(bioc_location)
return bioc_annotation
def add_annotation(triple, annotation_id):
# initialize annotation element
bioc_annotation = BioCAnnotation()
# MeSH term in a tag <text> ... </text> (origininal term, searched case insensitive)
bioc_annotation.text = triple[2]
# generate XML structure for the annotation and add infon
bioc_annotation.id = str(annotation_id)
bioc_annotation.put_infon('type', 'MeSH term')
# add location element
bioc_location = BioCLocation()
# add length of MeSH term
bioc_location.length = str(triple[1])
# add start position (offset)
bioc_location.offset = str(triple[0])
bioc_annotation.add_location(bioc_location)
return bioc_annotation
