gabrielaltay
commited on
Commit
•
9e0e587
1
Parent(s):
158149d
upload bigbiohub.py to hub from bigbio repo
Browse files- bigbiohub.py +37 -1
bigbiohub.py
CHANGED
@@ -163,6 +163,40 @@ kb_features = datasets.Features(
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def get_texts_and_offsets_from_bioc_ann(ann: "bioc.BioCAnnotation") -> Tuple:
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offsets = [(loc.offset, loc.offset + loc.length) for loc in ann.locations]
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@@ -304,9 +338,11 @@ def parse_brat_file(
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ann_lines = []
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for suffix in annotation_file_suffixes:
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annotation_file = txt_file.with_suffix(suffix)
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-
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with annotation_file.open() as f:
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ann_lines.extend(f.readlines())
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example["text_bound_annotations"] = []
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example["events"] = []
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)
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+
TASK_TO_SCHEMA = {
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Tasks.NAMED_ENTITY_RECOGNITION.name: "KB",
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Tasks.NAMED_ENTITY_DISAMBIGUATION.name: "KB",
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Tasks.EVENT_EXTRACTION.name: "KB",
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Tasks.RELATION_EXTRACTION.name: "KB",
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Tasks.COREFERENCE_RESOLUTION.name: "KB",
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Tasks.QUESTION_ANSWERING.name: "QA",
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Tasks.TEXTUAL_ENTAILMENT.name: "TE",
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Tasks.SEMANTIC_SIMILARITY.name: "PAIRS",
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Tasks.TEXT_PAIRS_CLASSIFICATION.name: "PAIRS",
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Tasks.PARAPHRASING.name: "T2T",
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Tasks.TRANSLATION.name: "T2T",
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Tasks.SUMMARIZATION.name: "T2T",
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Tasks.TEXT_CLASSIFICATION.name: "TEXT",
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}
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SCHEMA_TO_TASKS = defaultdict(set)
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for task, schema in TASK_TO_SCHEMA.items():
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SCHEMA_TO_TASKS[schema].add(task)
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SCHEMA_TO_TASKS = dict(SCHEMA_TO_TASKS)
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VALID_TASKS = set(TASK_TO_SCHEMA.keys())
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VALID_SCHEMAS = set(TASK_TO_SCHEMA.values())
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SCHEMA_TO_FEATURES = {
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"KB": kb_features,
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"QA": qa_features,
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"TE": entailment_features,
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"T2T": text2text_features,
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"TEXT": text_features,
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"PAIRS": pairs_features,
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}
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def get_texts_and_offsets_from_bioc_ann(ann: "bioc.BioCAnnotation") -> Tuple:
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offsets = [(loc.offset, loc.offset + loc.length) for loc in ann.locations]
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ann_lines = []
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for suffix in annotation_file_suffixes:
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annotation_file = txt_file.with_suffix(suffix)
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try:
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with annotation_file.open() as f:
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ann_lines.extend(f.readlines())
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except Exception:
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continue
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example["text_bound_annotations"] = []
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example["events"] = []
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