ncbi_disease.py

# 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
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# distributed under the License is distributed on an "AS IS" BASIS,
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# Lint as: python3
"""NCBI disease corpus: a resource for disease name recognition and concept normalization"""

import datasets


logger = datasets.logging.get_logger(__name__)


_CITATION = """\
@article{dougan2014ncbi,
         title={NCBI disease corpus: a resource for disease name recognition and concept normalization},
         author={Dogan, Rezarta Islamaj and Leaman, Robert and Lu, Zhiyong},
         journal={Journal of biomedical informatics},
         volume={47},
         pages={1--10},
         year={2014},
         publisher={Elsevier}
}
"""

_DESCRIPTION = """\
This paper presents the disease name and concept annotations of the NCBI disease corpus, a collection of 793 PubMed
abstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural
language processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions
and their corresponding concepts in Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man (OMIM®).
Manual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations.
Fourteen annotators were randomly paired and differing annotations were discussed for reaching a consensus in two
annotation phases. In this setting, a high inter-annotator agreement was observed. Finally, all results were checked
against annotations of the rest of the corpus to assure corpus-wide consistency.

For more details, see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951655/

The original dataset can be downloaded from: https://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/NCBI_corpus.zip
This dataset has been converted to CoNLL format for NER using the following tool: https://github.com/spyysalo/standoff2conll
Note: there is a duplicate document (PMID 8528200) in the original data, and the duplicate is recreated in the converted data.
"""

_HOMEPAGE = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951655/"
_URL = "https://github.com/spyysalo/ncbi-disease/raw/master/conll/"
_TRAINING_FILE = "train.tsv"
_DEV_FILE = "devel.tsv"
_TEST_FILE = "test.tsv"


class NCBIDiseaseConfig(datasets.BuilderConfig):
    """BuilderConfig for NCBIDisease"""

    def __init__(self, **kwargs):
        """BuilderConfig for NCBIDisease.
        Args:
          **kwargs: keyword arguments forwarded to super.
        """
        super(NCBIDiseaseConfig, self).__init__(**kwargs)


class NCBIDisease(datasets.GeneratorBasedBuilder):
    """NCBIDisease dataset."""

    BUILDER_CONFIGS = [
        NCBIDiseaseConfig(name="ncbi_disease", version=datasets.Version("1.0.0"), description="NCBIDisease dataset"),
    ]

    def _info(self):
        custom_names = ['O','B-GENE','I-GENE','B-CHEMICAL','I-CHEMICAL','B-DISEASE','I-DISEASE',
            'B-DNA', 'I-DNA', 'B-RNA', 'I-RNA', 'B-CELL_LINE', 'I-CELL_LINE', 'B-CELL_TYPE', 'I-CELL_TYPE', 
            'B-PROTEIN', 'I-PROTEIN', 'B-SPECIES', 'I-SPECIES'] 
        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=custom_names 
                        )
                    ),
                }
            ),
            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])
                    if(splits[1].rstrip()=="B-Disease"):
                        ner_tags.append("B-DISEASE")
                    elif(splits[1].rstrip()=="I-Disease"):
                        ner_tags.append("I-DISEASE")
                    else:
                        ner_tags.append(splits[1].rstrip())
            # last example
            yield guid, {
                "id": str(guid),
                "tokens": tokens,
                "ner_tags": ner_tags,
            }