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""" |
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MedQA Textbook (English) with focused emphasis on domain of Clinical Medicine and other subsets relevant for use with |
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Clinical Ontologies. |
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Textbooks: |
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Anatomy_Gray.txt Clinical medicine |
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Biochemistry_Lippincott.txt Basic biology |
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Cell_Biology_Alberts.txt Basic biology |
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First_Aid_Step1.txt Clinical medicine |
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First_Aid_Step2.txt Clinical medicine |
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Gynecology_Novak.txt Clinical medicine |
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Histology_Ross.txt Basic biology |
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Immunology_Janeway.txt Allergy and immunology Clinical medicine |
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InternalMed_Harrison.txt Clinical medicine |
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Neurology_Adams.txt Neurology Clinical medicine |
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Obstentrics_Williams.txt OBGYN Clinical medicine |
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Pathology_Robbins.txt Basic biology |
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Pathoma_Husain.txt Pathology Clinical medicine |
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Pediatrics_Nelson.txt Pediatrics Clinical medicine |
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Pharmacology_Katzung.txt Pharmacology |
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Physiology_Levy.txt Basic biology |
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Psichiatry_DSM-5.txt Psychiatry |
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Surgery_Schwartz.txt Surgery Clinical medicine |
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""" |
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SUBJECT_SUBSETS = { |
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"core_clinical": |
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["Anatomy_Gray", "First_Aid_Step1", "First_Aid_Step2", "Immunology_Janeway", |
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"InternalMed_Harrison", "Neurology_Adams", "Obstentrics_Williams", "Pathoma_Husain", "Pediatrics_Nelson", |
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"Surgery_Schwartz"], |
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"basic_biology": |
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["Biochemistry_Lippincott", "Cell_Biology_Alberts", "Histology_Ross", "Pathology_Robbins", "Physiology_Levy"], |
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"pharmacology": |
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["Pharmacology_Katzung"], |
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"psychiatry": |
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["Psichiatry_DSM-5"] |
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} |
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from pathlib import Path |
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import json |
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import datasets |
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CHUNK_OVERLAP = 20 |
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MAX_CHUNK_SIZE = 800 |
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_DESCRIPTION = """\ |
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MedQA Textbook (English) with emphasis on domain of Clinical Medicine and other subsets. |
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""" |
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_HOMEPAGE = "https://github.com/jind11/MedQA" |
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_LICENSE = """ |
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MIT License |
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Copyright (c) 2022 Di Jin |
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Permission is hereby granted, free of charge, to any person obtaining a copy |
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of this software and associated documentation files (the "Software"), to deal |
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in the Software without restriction, including without limitation the rights |
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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copies of the Software, and to permit persons to whom the Software is |
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furnished to do so, subject to the following conditions: |
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The above copyright notice and this permission notice shall be included in all |
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copies or substantial portions of the Software. |
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE |
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SOFTWARE. |
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""" |
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_URLS = ["textbooks_en_jsonl.zip"] |
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_CITATION = """\ |
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@article{jin2021disease, |
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title={What disease does this patient have? a large-scale open domain question answering dataset from medical exams}, |
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author={Jin, Di and Pan, Eileen and Oufattole, Nassim and Weng, Wei-Hung and Fang, Hanyi and Szolovits, Peter}, |
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journal={Applied Sciences}, |
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volume={11}, |
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number={14}, |
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pages={6421}, |
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year={2021}, |
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publisher={MDPI} |
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} |
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""" |
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def get_med_qa_textbooks(location, subset_name): |
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for textbook_content in location.glob('*.jsonl'): |
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textbook_name = textbook_content.name.split('.')[0] |
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if textbook_name in SUBJECT_SUBSETS[subset_name]: |
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with textbook_content.open("r") as fid: |
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for line in fid: |
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yield json.loads(line) |
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class MedQACorpus(datasets.GeneratorBasedBuilder): |
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"""MedQA Textbook (English) with emphasis on domain of Clinical Medicine and other subsets.""" |
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VERSION = datasets.Version("0.0.1") |
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BUILDER_CONFIGS = [ |
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datasets.BuilderConfig(name="core_clinical", version=VERSION, description="Core clinical medicine"), |
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datasets.BuilderConfig(name="basic_biology", version=VERSION, description="Basic biology"), |
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datasets.BuilderConfig(name="pharmacology", version=VERSION, description="Pharmacology"), |
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datasets.BuilderConfig(name="psychiatry", version=VERSION, description="Psychiatry") |
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] |
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DEFAULT_CONFIG_NAME = "core_clinical" |
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|
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def _info(self): |
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features = datasets.Features( |
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{ |
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"text": datasets.Value("string"), |
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"source": datasets.Value("string"), |
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} |
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) |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=features, |
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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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def _split_generators(self, dl_manager): |
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urls = _URLS[0] |
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data_dir = Path(dl_manager.download_and_extract(urls)) |
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self.base_dir = data_dir / "textbooks" / "en" |
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return [ |
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datasets.SplitGenerator(name=datasets.Split.TRAIN) |
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] |
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def _generate_examples(self): |
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for key, record in enumerate(get_med_qa_textbooks(self.base_dir, self.config.name)): |
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yield key, record |
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