lambda x: TSVstring2list(x, int), TSVstring2bool, no_op, no_op,
lambda x: TSVstring2list(x, int), TSVstring2bool, no_op
])
# Create the sentence object where the two mentions appear
sentence = Sentence(line_dict["doc_id"], line_dict["sent_id"],
line_dict["wordidxs"], line_dict["words"],
line_dict["poses"], line_dict["ners"],
line_dict["lemmas"], line_dict["dep_paths"],
line_dict["dep_parents"],
line_dict["bounding_boxes"])
# Create the mentions
gene_1_mention = Mention(
"GENE", line_dict["gene_1_entity"],
[sentence.words[j] for j in line_dict["gene_1_wordidxs"]])
gene_1_mention.is_correct = line_dict["gene_1_is_correct"]
gene_1_mention.type = line_dict["gene_1_type"]
gene_2_mention = Mention(
"GENE", line_dict["gene_2_entity"],
[sentence.words[j] for j in line_dict["gene_2_wordidxs"]])
gene_2_mention.is_correct = line_dict["gene_2_is_correct"]
gene_2_mention.type = line_dict["gene_2_type"]
# If the word indexes do not overlap, create the relation candidate
# TODO there may be other cases. Check with Emily.
if not set(line_dict["gene_1_wordidxs"]) & \
set(line_dict["gene_2_wordidxs"]):
relation = Relation("GENEGENE", gene_1_mention, gene_2_mention)
# Add features
add_features(relation, gene_1_mention, gene_2_mention,
sentence)
# Supervise
# One of the two mentions (or both) is labelled as False
TSVstring2list, lambda x: TSVstring2list(x, int),
TSVstring2list, no_op, lambda x: TSVstring2list(x, int),
TSVstring2bool, no_op, no_op, lambda x: TSVstring2list(x,
int), TSVstring2bool, no_op])
# Create the sentence object where the two mentions appear
sentence = Sentence(
line_dict["doc_id"], line_dict["sent_id"],
line_dict["wordidxs"], line_dict["words"], line_dict["poses"],
line_dict["ners"], line_dict["lemmas"], line_dict["dep_paths"],
line_dict["dep_parents"], line_dict["bounding_boxes"])
# Create the mentions
gene_1_mention = Mention(
"GENE", line_dict["gene_1_entity"],
[sentence.words[j] for j in line_dict["gene_1_wordidxs"]])
gene_1_mention.is_correct = line_dict["gene_1_is_correct"]
gene_1_mention.type = line_dict["gene_1_type"]
gene_2_mention = Mention(
"GENE", line_dict["gene_2_entity"],
[sentence.words[j] for j in line_dict["gene_2_wordidxs"]])
gene_2_mention.is_correct = line_dict["gene_2_is_correct"]
gene_2_mention.type = line_dict["gene_2_type"]
# If the word indexes do not overlap, create the relation candidate
# TODO there may be other cases. Check with Emily.
if not set(line_dict["gene_1_wordidxs"]) & \
set(line_dict["gene_2_wordidxs"]):
relation = Relation(
"GENEGENE", gene_1_mention, gene_2_mention)
# Add features
add_features(relation, gene_1_mention, gene_2_mention,
sentence)
# Supervise
# Iterate over each pair of (gene,phenotype) mention
for g_idx in range(len(line_dict["gene_is_corrects"])):
g_wordidxs = TSVstring2list(
line_dict["gene_wordidxss"][g_idx], int)
gene_mention = Mention(
"GENE", line_dict["gene_entities"][g_idx],
[sentence.words[j] for j in g_wordidxs])
if line_dict["gene_is_corrects"][g_idx] == "n":
gene_mention.is_correct = None
elif line_dict["gene_is_corrects"][g_idx] == "f":
gene_mention.is_correct = False
elif line_dict["gene_is_corrects"][g_idx] == "t":
gene_mention.is_correct = True
else:
assert False
gene_mention.type = line_dict["gene_types"][g_idx]
assert not gene_mention.type.endswith("_UNSUP")
for h_idx in range(len(line_dict["hpoterm_is_corrects"])):
h_wordidxs = TSVstring2list(
line_dict["hpoterm_wordidxss"][h_idx], int)
hpoterm_mention = Mention(
"hpoterm", line_dict["hpoterm_entities"][h_idx],
[sentence.words[j] for j in h_wordidxs])
if line_dict["hpoterm_is_corrects"][h_idx] == "n":
hpoterm_mention.is_correct = None
elif line_dict["hpoterm_is_corrects"][h_idx] == "f":
hpoterm_mention.is_correct = False
elif line_dict["hpoterm_is_corrects"][h_idx] == "t":
hpoterm_mention.is_correct = True
else:
assert False
# Iterate over each pair of (gene,phenotype) mention
for g_idx in range(len(line_dict["gene_is_corrects"])):
g_wordidxs = TSVstring2list(line_dict["gene_wordidxss"][g_idx],
int)
gene_mention = Mention("GENE",
line_dict["gene_entities"][g_idx],
[sentence.words[j] for j in g_wordidxs])
if line_dict["gene_is_corrects"][g_idx] == "n":
gene_mention.is_correct = None
elif line_dict["gene_is_corrects"][g_idx] == "f":
gene_mention.is_correct = False
elif line_dict["gene_is_corrects"][g_idx] == "t":
gene_mention.is_correct = True
else:
assert False
gene_mention.type = line_dict["gene_types"][g_idx]
assert not gene_mention.type.endswith("_UNSUP")
for h_idx in range(len(line_dict["hpoterm_is_corrects"])):
h_wordidxs = TSVstring2list(
line_dict["hpoterm_wordidxss"][h_idx], int)
hpoterm_mention = Mention(
"hpoterm", line_dict["hpoterm_entities"][h_idx],
[sentence.words[j] for j in h_wordidxs])
if line_dict["hpoterm_is_corrects"][h_idx] == "n":
hpoterm_mention.is_correct = None
elif line_dict["hpoterm_is_corrects"][h_idx] == "f":
hpoterm_mention.is_correct = False
elif line_dict["hpoterm_is_corrects"][h_idx] == "t":
hpoterm_mention.is_correct = True
else:
assert False
