gabrielaltay commited on
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e33226d
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upload bigbiohub.py to hub from bigbio repo

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  1. bigbiohub.py +153 -0
bigbiohub.py ADDED
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+ from dataclasses import dataclass
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+ from enum import Enum
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+ import datasets
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+ from types import SimpleNamespace
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+
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+
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+ BigBioValues = SimpleNamespace(NULL="<BB_NULL_STR>")
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+
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+
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+ @dataclass
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+ class BigBioConfig(datasets.BuilderConfig):
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+ """BuilderConfig for BigBio."""
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+
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+ name: str = None
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+ version: datasets.Version = None
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+ description: str = None
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+ schema: str = None
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+ subset_id: str = None
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+
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+
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+ class Tasks(Enum):
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+ NAMED_ENTITY_RECOGNITION = "NER"
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+ NAMED_ENTITY_DISAMBIGUATION = "NED"
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+ EVENT_EXTRACTION = "EE"
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+ RELATION_EXTRACTION = "RE"
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+ COREFERENCE_RESOLUTION = "COREF"
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+ QUESTION_ANSWERING = "QA"
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+ TEXTUAL_ENTAILMENT = "TE"
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+ SEMANTIC_SIMILARITY = "STS"
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+ TEXT_PAIRS_CLASSIFICATION = "TXT2CLASS"
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+ PARAPHRASING = "PARA"
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+ TRANSLATION = "TRANSL"
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+ SUMMARIZATION = "SUM"
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+ TEXT_CLASSIFICATION = "TXTCLASS"
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+
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+
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+ entailment_features = datasets.Features(
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+ {
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+ "id": datasets.Value("string"),
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+ "premise": datasets.Value("string"),
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+ "hypothesis": datasets.Value("string"),
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+ "label": datasets.Value("string"),
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+ }
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+ )
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+
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+ pairs_features = datasets.Features(
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+ {
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+ "id": datasets.Value("string"),
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+ "document_id": datasets.Value("string"),
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+ "text_1": datasets.Value("string"),
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+ "text_2": datasets.Value("string"),
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+ "label": datasets.Value("string"),
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+ }
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+ )
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+
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+ qa_features = datasets.Features(
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+ {
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+ "id": datasets.Value("string"),
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+ "question_id": datasets.Value("string"),
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+ "document_id": datasets.Value("string"),
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+ "question": datasets.Value("string"),
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+ "type": datasets.Value("string"),
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+ "choices": [datasets.Value("string")],
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+ "context": datasets.Value("string"),
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+ "answer": datasets.Sequence(datasets.Value("string")),
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+ }
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+ )
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+
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+ text_features = datasets.Features(
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+ {
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+ "id": datasets.Value("string"),
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+ "document_id": datasets.Value("string"),
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+ "text": datasets.Value("string"),
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+ "labels": [datasets.Value("string")],
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+ }
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+ )
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+
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+ text2text_features = datasets.Features(
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+ {
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+ "id": datasets.Value("string"),
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+ "document_id": datasets.Value("string"),
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+ "text_1": datasets.Value("string"),
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+ "text_2": datasets.Value("string"),
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+ "text_1_name": datasets.Value("string"),
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+ "text_2_name": datasets.Value("string"),
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+ }
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+ )
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+
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+ kb_features = datasets.Features(
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+ {
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+ "id": datasets.Value("string"),
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+ "document_id": datasets.Value("string"),
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+ "passages": [
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+ {
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+ "id": datasets.Value("string"),
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+ "type": datasets.Value("string"),
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+ "text": datasets.Sequence(datasets.Value("string")),
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+ "offsets": datasets.Sequence([datasets.Value("int32")]),
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+ }
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+ ],
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+ "entities": [
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+ {
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+ "id": datasets.Value("string"),
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+ "type": datasets.Value("string"),
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+ "text": datasets.Sequence(datasets.Value("string")),
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+ "offsets": datasets.Sequence([datasets.Value("int32")]),
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+ "normalized": [
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+ {
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+ "db_name": datasets.Value("string"),
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+ "db_id": datasets.Value("string"),
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+ }
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+ ],
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+ }
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+ ],
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+ "events": [
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+ {
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+ "id": datasets.Value("string"),
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+ "type": datasets.Value("string"),
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+ # refers to the text_bound_annotation of the trigger
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+ "trigger": {
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+ "text": datasets.Sequence(datasets.Value("string")),
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+ "offsets": datasets.Sequence([datasets.Value("int32")]),
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+ },
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+ "arguments": [
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+ {
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+ "role": datasets.Value("string"),
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+ "ref_id": datasets.Value("string"),
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+ }
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+ ],
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+ }
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+ ],
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+ "coreferences": [
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+ {
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+ "id": datasets.Value("string"),
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+ "entity_ids": datasets.Sequence(datasets.Value("string")),
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+ }
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+ ],
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+ "relations": [
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+ {
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+ "id": datasets.Value("string"),
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+ "type": datasets.Value("string"),
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+ "arg1_id": datasets.Value("string"),
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+ "arg2_id": datasets.Value("string"),
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+ "normalized": [
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+ {
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+ "db_name": datasets.Value("string"),
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+ "db_id": datasets.Value("string"),
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+ }
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+ ],
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+ }
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+ ],
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+ }
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+ )