bc7_litcovid.py

# 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.

from typing import Dict, List, Tuple

import datasets
import pandas as pd

from .bigbiohub import BigBioConfig, Tasks, text_features

_LANGUAGES = ["English"]
_PUBMED = True
_LOCAL = False
_CITATION = """\
@inproceedings{chen2021overview,
  title        = {
    Overview of the BioCreative VII LitCovid Track: multi-label topic
    classification for COVID-19 literature annotation
  },
  author       = {
    Chen, Qingyu and Allot, Alexis and Leaman, Robert and Do{\\u{g}}an, Rezarta
    Islamaj and Lu, Zhiyong
  },
  year         = 2021,
  booktitle    = {Proceedings of the seventh BioCreative challenge evaluation workshop}
}

"""

_DATASETNAME = "bc7_litcovid"
_DISPLAYNAME = "BC7-LitCovid"

_DESCRIPTION = """\
The training and development datasets contain the publicly-available \
text of over 30 thousand COVID-19-related articles and their metadata \
(e.g., title, abstract, journal). Articles in both datasets have been \
manually reviewed and articles annotated by in-house models.
"""

_HOMEPAGE = "https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-5/"

_LICENSE = "UNKNOWN"

_BASE = "https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/BC7-LitCovid-"

_URLS = {
    _DATASETNAME: {
        "train": _BASE + "Train.csv",
        "validation": _BASE + "Dev.csv",
        "test": _BASE + "Test-GS.csv",
    },
}

_SUPPORTED_TASKS = [Tasks.TEXT_CLASSIFICATION]

_SOURCE_VERSION = "1.0.0"
_BIGBIO_VERSION = "1.0.0"

_CLASS_NAMES = [
    "Epidemic Forecasting",
    "Treatment",
    "Prevention",
    "Mechanism",
    "Case Report",
    "Transmission",
    "Diagnosis",
]

logger = datasets.utils.logging.get_logger(__name__)


class BC7LitCovidDataset(datasets.GeneratorBasedBuilder):
    """
    Track 5 - LitCovid track Multi-label topic classification for
    COVID-19 literature annotation
    """

    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)

    BUILDER_CONFIGS = [
        BigBioConfig(
            name="bc7_litcovid_source",
            version=SOURCE_VERSION,
            description="bc7_litcovid source schema",
            schema="source",
            subset_id="bc7_litcovid",
        ),
        BigBioConfig(
            name="bc7_litcovid_bigbio_text",
            version=BIGBIO_VERSION,
            description="bc7_litcovid BigBio schema",
            schema="bigbio_text",
            subset_id="bc7_litcovid",
        ),
    ]

    DEFAULT_CONFIG_NAME = "bc7_litcovid_source"

    def _info(self) -> datasets.DatasetInfo:

        if self.config.schema == "source":

            features = datasets.Features(
                {
                    "pmid": datasets.Value("string"),
                    "journal": datasets.Value("string"),
                    "title": datasets.Value("string"),
                    "abstract": datasets.Value("string"),
                    "keywords": datasets.Sequence(datasets.Value("string")),
                    "pub_type": datasets.Sequence(datasets.Value("string")),
                    "authors": datasets.Sequence(datasets.Value("string")),
                    "doi": datasets.Value("string"),
                    "labels": datasets.Sequence(datasets.ClassLabel(names=_CLASS_NAMES)),
                }
            )

        elif self.config.schema == "bigbio_text":
            features = text_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."""

        # Download all the CSV
        urls = _URLS[_DATASETNAME]
        path_train = dl_manager.download(urls["train"])
        path_validation = dl_manager.download(urls["validation"])
        path_test = dl_manager.download(urls["test"])

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                gen_kwargs={
                    "filepath": path_train,
                    "split": "train",
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.TEST,
                gen_kwargs={
                    "filepath": path_validation,
                    "split": "test",
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.VALIDATION,
                gen_kwargs={
                    "filepath": path_test,
                    "split": "dev",
                },
            ),
        ]

    def _validate_entry(self, e, index) -> bool:
        """
        Validates if an entry has all the required fields
        """
        fields_to_validate = ["pmid", "abstract", "label"]
        for key in fields_to_validate:
            if e[key]:
                continue
            else:
                logger.warning(f"Entry {index} missing {key}")
                return False
        return True

    def _generate_examples(self, filepath, split: str) -> Tuple[int, Dict]:
        """Yields examples as (key, example) tuples."""

        idx = 0

        # Load the CSV and convert it to the string format
        df = pd.read_csv(filepath, sep=",").astype(str).replace({"nan": None})

        for index, e in df.iterrows():
            if not self._validate_entry(e, index):
                continue
            if self.config.schema == "source":

                yield idx, {
                    "pmid": e["pmid"],
                    "journal": e["journal"],
                    "title": e["title"],
                    "abstract": e["abstract"],
                    "keywords": e["keywords"].split(";") if e["keywords"] is not None else [],
                    "pub_type": e["pub_type"].split(";") if e["pub_type"] is not None else [],
                    "authors": e["authors"].split(";") if e["authors"] is not None else [],
                    "doi": e["doi"],
                    "labels": e["label"].split(";"),
                }

            elif self.config.schema == "bigbio_text":

                yield idx, {
                    "id": idx,
                    "document_id": e["pmid"],
                    "text": e["abstract"],
                    "labels": e["label"].split(";"),
                }

            idx += 1