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Create sci_lay.py

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+ """SciLay Dataset."""
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+
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+ import gzip
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+ import json
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+ import os
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+
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+ import datasets
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+ from datasets.download.streaming_download_manager import FilesIterable
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+
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+ _HOMEPAGE = ""
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+
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+ _CITATION = """
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+ """
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+
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+ _DESCRIPTION = """
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+ SCILAY comprises 46,486 instances, each representing a scientific article in the biomedical domain.
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+ Each instance in the dataset includes the following components:
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+ - plain_text: Containing a plain language summary of the scientific article. This section is written in a simple and accessible language, and is intended to be understandable by a wide audience.
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+ - technical_text: This section contains the abstract of the scientific article. It provides a detailed and technical description of the research conducted in the article.
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+ In addition to the textual content, each instance is associated with the following metadata:
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+ - Keywords: Keywords that capture the main topics and themes addressed in the article.
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+ - Journal: The journal in which the article is published, providing context about the source of the research.
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+ - DOI (Digital Object Identifier): A unique identifier for the article, facilitating easy referencing.
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+ The main objective of the SCILAY dataset is to support the development and evaluation of text summarization models that can effectively simplify complex scientific language while retaining the essential information.
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+ """
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+
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+ _LICENSE = "Creative Commons Attribution 4.0 International"
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+
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+ _SPLIT_NAMES = {datasets.Split.TRAIN: "train", datasets.Split.VALIDATION: "validation", datasets.Split.TEST: "test"}
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+ _URL = "data/{version}/{split_name}.zip"
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+
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+ _DOI = "doi"
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+ _PMCID = "pmcid"
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+ _SUMMARY = "plain_text"
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+ _ABSTRACT = "technical_text"
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+ _JOURNAL = "journal"
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+ _TOPICS = "topics"
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+ _KEYWORDS = "keywords"
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+
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+ _JOURNALS = {
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+ "NC": "Nature Communications",
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+ "A": "Animals: an Open Access Journal from MDPI",
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+ "NIHR": "NIHR Journals Library",
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+ "PLGEN": "PLoS Genetics",
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+ "PLPAT": "PLoS Pathogens",
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+ "PLCB": "PLoS Computational Biology",
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+ "PLNTD": "PLoS Neglected Tropical Diseases",
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+ "B": "Biology",
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+ "I": "Insects",
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+ "EL": "eLife",
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+ "PLB": "PLoS Biology",
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+ "CB": "Communications Biology",
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+ "SD": "Scientific Data",
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+ "MBIO": "mBio",
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+ "C": "Cancers",
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+ "OTHER": "Others"
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+ }
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+
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+ # Available versions:
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+ # 1.0.0 cased raw strings.
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+
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+ _VERSION = "1.0.0"
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+
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+ class SciLayConfig(datasets.BuilderConfig):
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+ """BuilderConfig for SciLay."""
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+
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+ def __init__(self, journals="all", version=_VERSION, **kwargs):
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+ """BuilderConfig for SciLay.
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+ Args:
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+ journals (str or list, default 'all'): List of journal names. Either 'all' or a combination
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+ of {'NC', 'A', 'NIHR', 'PLGEN', 'PLPAT', 'PLCB', 'PLNTD', 'B', 'I', 'EL', 'PLB', 'CB', 'SD', 'MBIO', 'C', 'OTHER'}.
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+ **kwargs: keyword arguments forwarded to super.
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+ """
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+ if isinstance(journals, str):
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+ journals = [journals]
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+ name = "+".join(journals)
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+ if name == "all":
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+ journals = list(_JOURNALS)
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+ if version != _VERSION:
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+ name = f"{name}-{version}"
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+ super().__init__(name=name, version=version, **kwargs)
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+ self.journals = journals
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+
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+ class SciLay(datasets.GeneratorBasedBuilder):
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+ """SciLay datasets."""
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+
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+ BUILDER_CONFIG_CLASS = SciLayConfig
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+ BUILDER_CONFIGS = [
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+ SciLayConfig(
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+ journals="all",
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+ description="Articles from all journals.",
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+ ),
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+ ] + [
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+ SciLayConfig(
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+ journals=k,
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+ description=f"Articles from journals {k}: {v}",
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+ )
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+ for k, v in sorted(_JOURNALS.items())
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+ ]
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+ DEFAULT_CONFIG_NAME = "all"
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+ VERSION = _VERSION
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+
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+ def _info(self):
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+ return datasets.DatasetInfo(
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+ description=_DESCRIPTION,
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+ features=datasets.Features({
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+ _DOI: datasets.Value("string"),
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+ _PMCID: datasets.Value("string"),
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+ _SUMMARY: datasets.Value("string"),
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+ _ABSTRACT: datasets.Value("string"),
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+ _JOURNAL: datasets.Value("string"),
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+ _TOPICS: datasets.Sequence(datasets.Value("string")),
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+ _KEYWORDS: datasets.Sequence(datasets.Value("string"))
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+ }),
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+ supervised_keys=(_ABSTRACT, _SUMMARY),
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+ homepage=_HOMEPAGE,
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+ license=_LICENSE,
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+ citation=_CITATION,
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+ )
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+
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+ def _split_generators(self, dl_manager):
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+ """Returns SplitGenerators."""
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+ urls = {
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+ split: _URL.format(version=self.config.version, split_name=split_name)
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+ for split, split_name in _SPLIT_NAMES.items()
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+ }
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+ dl_paths = dl_manager.download_and_extract(urls)
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+ paths = {
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+ split: [
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+ dl_manager.iter_files(os.path.join(dl_paths[split], split_name, code)) for code in self.config.journals
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+ ]
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+ for split, split_name in _SPLIT_NAMES.items()
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+ }
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+ raise Exception(f"paths creati = {[file_path.__repr__ for file_path in paths]}")
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+ return [
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+ datasets.SplitGenerator(
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+ name=split,
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+ gen_kwargs={"paths": paths[split]},
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+ )
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+ for split in _SPLIT_NAMES
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+ ]
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+
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+ def _generate_examples(self, paths=None):
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+ """Yields examples."""
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+ for paths_per_journal in paths:
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+ for path in paths_per_journal:
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+ with open(path, "rb") as fin:
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+ fin = gzip.GzipFile(fileobj=fin)
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+ for row in fin:
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+ json_obj = json.loads(row)
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+ yield json_obj["doi"], {
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+ _DOI: json_obj[_DOI],
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+ _PMCID: json_obj[_PMCID],
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+ _SUMMARY: json_obj[_SUMMARY],
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+ _ABSTRACT: json_obj[_ABSTRACT],
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+ _JOURNAL: json_obj[_JOURNAL],
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+ _TOPICS: json_obj[_TOPICS],
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+ _KEYWORDS: json_obj[_KEYWORDS]
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+ }
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+