def convert_pubtator(input_path, output_path):
"""Convert pubtators annotation list to BioC XML
Keyword Arguments:
input_file -- the path of pubtators annotation file
output_file -- the path to output the BioC XML file
"""
# Set up BioCWriter to write specifically Pubtator
# Can change to incorporate other sources besides pubtator
writer = BioCWriter()
writer.collection = BioCCollection()
collection = writer.collection
collection.date = time.strftime("%Y/%m/%d")
collection.source = "Pubtator"
collection.key = "Pubtator.key"
opener = utilities.get_opener(output_path)
with opener(output_path, 'wb') as xml_file:
# Have to manually do this because hangs otherwise
# Write the head of the xml file
xml_shell = writer.tostring('UTF-8')
*xml_head, xml_tail = xml_shell.rstrip().split(b'\n')
for line in xml_head:
xml_file.write(line + b'\n')
article_generator = read_bioconcepts2pubtator_offsets(input_path)
# Write each article in BioC format
for article in tqdm.tqdm(article_generator):
document = BioCDocument()
document.id = article["pubmed_id"]
title_passage = BioCPassage()
title_passage.put_infon('type', 'title')
title_passage.offset = '0'
title_passage.text = article["title"]
abstract_passage = BioCPassage()
abstract_passage.put_infon('type', 'abstract')
abstract_passage.offset = article["abstract"]
abstract_passage.text = article["abstract"]
id_index = 0
for tag in article["title_annot"]:
title_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
for tag in article["abstract_annot"]:
abstract_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
document.add_passage(title_passage)
document.add_passage(abstract_passage)
step_parent = E('collection')
writer._build_documents([document], step_parent)
xml_file.write(tostring(step_parent[0], pretty_print=True))
step_parent.clear()
# Write the closing tag of the xml document
xml_file.write(xml_tail + b'\n')
def convert_pubtator(input_file, output_file=None):
"""Convert pubtators annotation list to BioC XML
Keyword Arguments:
input_file -- the path of pubtators annotation file
output_file -- the path to output the converted text
"""
if output_file is None:
output_file = "bioc-converted-docs.xml"
# Set up BioCWriter to write specifically Pubtator
# Can change to incorporate other sources besides pubtator
writer = BioCWriter()
writer.collection = BioCCollection()
collection = writer.collection
collection.date = time.strftime("%Y/%m/%d")
collection.source = "Pubtator"
collection.key = "Pubtator.key"
with open(output_file, 'wb') as g:
# Have to manually do this because hangs otherwise
# Write the head of the xml file
xml_header = writer.tostring('UTF-8')
xml_tail = '</collection>\n'
xml_head = xml_header[:-len(xml_tail)]
g.write(xml_head)
article_generator = bioconcepts2pubtator_offsets(input_file)
# Write each article in BioC format
for article in tqdm.tqdm(article_generator):
document = BioCDocument()
document.id = article["Document ID"]
title_passage = BioCPassage()
title_passage.put_infon('type', 'title')
title_passage.offset = '0'
title_passage.text = article["Title"]
abstract_passage = BioCPassage()
abstract_passage.put_infon('type', 'abstract')
abstract_passage.offset = str(article["Abstract"])
abstract_passage.text = article["Abstract"]
id_index = 0
for tag in article["Title_Annot"]:
title_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
for tag in article["Abstract_Annot"]:
abstract_passage.annotations.append(bioconcepts2pubtator_annotations(tag, id_index))
id_index += 1
document.add_passage(title_passage)
document.add_passage(abstract_passage)
step_parent = E('collection')
writer._build_documents([document], step_parent)
g.write(tostring(step_parent[0], pretty_print=True))
step_parent.clear()
# Write the closing tag of the xml document
g.write(xml_tail)
