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# coding=utf-8
# Copyright 2022 The HuggingFace Datasets Authors and the current dataset script contributor.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
A dataset loading script for the Complex Named Entity Corpus (CoNECo.)
CoNECo is an annotated corpus for NER and NEN of protein-containing complexes. \
CoNECo comprises 1,621 documents with 2,052 entities, 1,976 of which are normalized \
to Gene Ontology. We divided the corpus into training, development, and test sets.
"""
from pathlib import Path
from typing import Dict, List, Tuple
import datasets
from .bigbiohub import (BigBioConfig, Tasks, brat_parse_to_bigbio_kb,
kb_features, parse_brat_file)
_LANGUAGES = ["English"]
_PUBMED = False
_LOCAL = False
_CITATION = """\
@article{10.1093/bioadv/vbae116,
author = {Nastou, Katerina and Koutrouli, Mikaela and Pyysalo, Sampo and Jensen, Lars Juhl},
title = "{CoNECo: A Corpus for Named Entity Recognition and Normalization of Protein Complexes}",
journal = {Bioinformatics Advances},
pages = {vbae116},
year = {2024},
month = {08},
abstract = "{Despite significant progress in biomedical information extraction, there is a lack of resources \
for Named Entity Recognition (NER) and Normalization (NEN) of protein-containing complexes. Current resources \
inadequately address the recognition of protein-containing complex names across different organisms, underscoring \
the crucial need for a dedicated corpus.We introduce the Complex Named Entity Corpus (CoNECo), an annotated \
corpus for NER and NEN of complexes. CoNECo comprises 1,621 documents with 2,052 entities, 1,976 of which are \
normalized to Gene Ontology. We divided the corpus into training, development, and test sets and trained both a \
transformer-based and dictionary-based tagger on them. Evaluation on the test set demonstrated robust performance, \
with F-scores of 73.7\\% and 61.2\\%, respectively. Subsequently, we applied the best taggers for comprehensive \
tagging of the entire openly accessible biomedical literature.All resources, including the annotated corpus, \
training data, and code, are available to the community through Zenodo https://zenodo.org/records/11263147 and \
GitHub https://zenodo.org/records/10693653.}",
issn = {2635-0041},
doi = {10.1093/bioadv/vbae116},
url = {https://doi.org/10.1093/bioadv/vbae116},
eprint = {https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbae116/\
58869902/vbae116.pdf},
}
"""
_DATASETNAME = "coneco"
_DISPLAYNAME = "CoNECo"
_DESCRIPTION = """\
Complex Named Entity Corpus (CoNECo) is an annotated corpus for NER and NEN of protein-containing complexes. \
CoNECo comprises 1,621 documents with 2,052 entities, 1,976 of which are normalized to Gene Ontology. We \
divided the corpus into training, development, and test sets.
"""
_HOMEPAGE = "https://zenodo.org/records/11263147"
_LICENSE = "CC_BY_4p0"
_URLS = {
_DATASETNAME: "https://zenodo.org/records/11263147/files/CoNECo_corpus.tar.gz?download=1",
}
_SUPPORTED_TASKS = [
Tasks.NAMED_ENTITY_RECOGNITION,
Tasks.NAMED_ENTITY_DISAMBIGUATION,
]
_SOURCE_VERSION = "2.0.0"
_BIGBIO_VERSION = "1.0.0"
class ConecoDataset(datasets.GeneratorBasedBuilder):
"""TODO: Short description of my dataset."""
SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
BUILDER_CONFIGS = [
BigBioConfig(
name="coneco_source",
version=SOURCE_VERSION,
description="coneco source schema",
schema="source",
subset_id="coneco",
),
BigBioConfig(
name="coneco_bigbio_kb",
version=BIGBIO_VERSION,
description="coneco BigBio schema",
schema="bigbio_kb",
subset_id="coneco",
),
]
DEFAULT_CONFIG_NAME = "coneco_source"
def _info(self) -> datasets.DatasetInfo:
if self.config.schema == "source":
features = datasets.Features(
{
"id": datasets.Value("string"),
"document_id": datasets.Value("string"),
"text": datasets.Value("string"),
"text_bound_annotations": [ # T line in brat, i.e. entities for NER task
{
"offsets": datasets.Sequence([datasets.Value("int32")]),
"text": datasets.Sequence(datasets.Value("string")),
"type": datasets.Value("string"),
"id": datasets.Value("string"),
}
],
"normalizations": [ # N lines in brat, i.e. normalization for NEN task
{
"id": datasets.Value("string"),
"type": datasets.Value("string"),
"ref_id": datasets.Value("string"),
"resource_name": datasets.Value("string"),
"cuid": datasets.Value("string"),
"text": datasets.Value("string"),
}
],
}
)
elif self.config.schema == "bigbio_kb":
features = kb_features
return datasets.DatasetInfo(
description=_DESCRIPTION,
features=features,
homepage=_HOMEPAGE,
license=str(_LICENSE),
citation=_CITATION,
)
def _split_generators(self, dl_manager) -> List[datasets.SplitGenerator]:
"""Returns SplitGenerators."""
urls = _URLS[_DATASETNAME]
data_dir = Path(dl_manager.download_and_extract(urls))
return [
datasets.SplitGenerator(
name=datasets.Split.TRAIN,
# Whatever you put in gen_kwargs will be passed to _generate_examples
gen_kwargs={
"filepath": data_dir / "train",
"split": "train",
},
),
datasets.SplitGenerator(
name=datasets.Split.TEST,
gen_kwargs={
"filepath": data_dir / "test",
"split": "test",
},
),
datasets.SplitGenerator(
name=datasets.Split.VALIDATION,
gen_kwargs={
"filepath": data_dir / "dev",
"split": "dev",
},
),
]
def _filter_oos_entities(self, brat_parse):
"""Filter out entity annotations with out-of-scope type."""
brat_parse["text_bound_annotations"] = [a for a in brat_parse["text_bound_annotations"] if a["type"] != "OOS"]
return brat_parse
def _generate_examples(self, filepath, split: str) -> Tuple[int, Dict]:
"""Yields examples as (key, example) tuples."""
if self.config.schema == "source":
for file in sorted(filepath.iterdir()):
if file.suffix != ".txt":
continue
brat_parsed = parse_brat_file(file)
brat_parsed = self._filter_oos_entities(brat_parsed)
brat_parsed["id"] = file.stem
yield brat_parsed["document_id"], brat_parsed
elif self.config.schema == "bigbio_kb":
for file in sorted(filepath.iterdir()):
if file.suffix != ".txt":
continue
brat_parsed = parse_brat_file(file)
brat_parsed = self._filter_oos_entities(brat_parsed)
bigbio_kb_example = brat_parse_to_bigbio_kb(brat_parsed)
bigbio_kb_example["id"] = file.stem
yield bigbio_kb_example["id"], bigbio_kb_example
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