Datasets:
Tasks:
Token Classification
Modalities:
Text
Formats:
parquet
Sub-tasks:
named-entity-recognition
Languages:
English
Size:
10K - 100K
License:
File size: 5,514 Bytes
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# coding=utf-8
# Copyright 2020 HuggingFace Datasets Authors.
#
# 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.
# Lint as: python3
"""BioCreative II gene mention recognition Corpus"""
import datasets
logger = datasets.logging.get_logger(__name__)
_CITATION = """\
@article{smith2008overview,
title={Overview of BioCreative II gene mention recognition},
author={Smith, Larry and Tanabe, Lorraine K and nee Ando, Rie Johnson and Kuo, Cheng-Ju and Chung, I-Fang and Hsu, Chun-Nan and Lin, Yu-Shi and Klinger, Roman and Friedrich, Christoph M and Ganchev, Kuzman and others},
journal={Genome biology},
volume={9},
number={S2},
pages={S2},
year={2008},
publisher={Springer}
}
"""
_DESCRIPTION = """\
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop.
In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions.
A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721.
Here we present brief descriptions of all the methods used and a statistical analysis of the results.
We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible,
and furthermore that the best result makes use of the lowest scoring submissions.
For more details, see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559986/
The original dataset can be downloaded from: https://biocreative.bioinformatics.udel.edu/resources/corpora/biocreative-ii-corpus/
This dataset has been converted to CoNLL format for NER using the following tool: https://github.com/spyysalo/standoff2conll
"""
_HOMEPAGE = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559986/"
_URL = "https://github.com/spyysalo/bc2gm-corpus/raw/master/conll/"
_TRAINING_FILE = "train.tsv"
_DEV_FILE = "devel.tsv"
_TEST_FILE = "test.tsv"
class Bc2gmCorpusConfig(datasets.BuilderConfig):
"""BuilderConfig for Bc2gmCorpus"""
def __init__(self, **kwargs):
"""BuilderConfig for Bc2gmCorpus.
Args:
**kwargs: keyword arguments forwarded to super.
"""
super(Bc2gmCorpusConfig, self).__init__(**kwargs)
class Bc2gmCorpus(datasets.GeneratorBasedBuilder):
"""Bc2gmCorpus dataset."""
BUILDER_CONFIGS = [
Bc2gmCorpusConfig(name="bc2gm_corpus", version=datasets.Version("1.0.0"), description="bc2gm corpus"),
]
def _info(self):
return datasets.DatasetInfo(
description=_DESCRIPTION,
features=datasets.Features(
{
"id": datasets.Value("string"),
"tokens": datasets.Sequence(datasets.Value("string")),
"ner_tags": datasets.Sequence(
datasets.features.ClassLabel(
names=[
"O",
"B-GENE",
"I-GENE",
]
)
),
}
),
supervised_keys=None,
homepage=_HOMEPAGE,
citation=_CITATION,
)
def _split_generators(self, dl_manager):
"""Returns SplitGenerators."""
urls_to_download = {
"train": f"{_URL}{_TRAINING_FILE}",
"dev": f"{_URL}{_DEV_FILE}",
"test": f"{_URL}{_TEST_FILE}",
}
downloaded_files = dl_manager.download_and_extract(urls_to_download)
return [
datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["train"]}),
datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": downloaded_files["dev"]}),
datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": downloaded_files["test"]}),
]
def _generate_examples(self, filepath):
logger.info("⏳ Generating examples from = %s", filepath)
with open(filepath, encoding="utf-8") as f:
guid = 0
tokens = []
ner_tags = []
for line in f:
if line == "" or line == "\n":
if tokens:
yield guid, {
"id": str(guid),
"tokens": tokens,
"ner_tags": ner_tags,
}
guid += 1
tokens = []
ner_tags = []
else:
# tokens are tab separated
splits = line.split("\t")
tokens.append(splits[0])
ner_tags.append(splits[1].rstrip())
# last example
if tokens:
yield guid, {
"id": str(guid),
"tokens": tokens,
"ner_tags": ner_tags,
}
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