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YAML Metadata Warning:The task_categories "text2text-generation" is not in the official list: text-classification, token-classification, table-question-answering, question-answering, zero-shot-classification, translation, summarization, feature-extraction, text-generation, fill-mask, sentence-similarity, text-to-speech, text-to-audio, automatic-speech-recognition, audio-to-audio, audio-classification, audio-text-to-text, voice-activity-detection, depth-estimation, image-classification, object-detection, image-segmentation, text-to-image, image-to-text, image-to-image, image-to-video, unconditional-image-generation, video-classification, reinforcement-learning, robotics, tabular-classification, tabular-regression, tabular-to-text, table-to-text, multiple-choice, text-ranking, text-retrieval, time-series-forecasting, text-to-video, image-text-to-text, image-text-to-image, image-text-to-video, visual-question-answering, document-question-answering, zero-shot-image-classification, graph-ml, mask-generation, zero-shot-object-detection, text-to-3d, image-to-3d, image-feature-extraction, video-text-to-text, keypoint-detection, visual-document-retrieval, any-to-any, video-to-video, other
PubMed Bioinformatics Abstracts (2020–2026)
A curated collection of 174,154 bioinformatics journal article abstracts from PubMed, covering publications from 2020 to 2026.
Curated by: Dr. Yash M Gupta
Intended Use
Fine-tuning large language models (LLMs) on biomedical / bioinformatics domain text.
Dataset Structure
| Column | Type | Description |
|---|---|---|
pmid |
string | PubMed ID |
title |
string | Article title |
abstract |
string | Full abstract text |
year |
string | Publication year |
journal |
string | Journal name |
doi |
string | DOI (if available) |
source |
string | Always "pubmed" |
slice |
string | Time slice used during collection |
Collection Method
- Source: NCBI PubMed via Entrez E-utilities (Biopython)
- Query:
bioinformatics[MeSH Terms] AND hasabstract[text] AND journal article[pt] - Date range: 2020–2026 (date of publication)
- Filters: Only articles with abstracts; journal articles only
License
This dataset is released under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.
The abstracts themselves are sourced from PubMed/MEDLINE and are subject to the NLM Terms and Conditions. Users must comply with NCBI/NLM usage policies when redistributing or using this data.
Citation
If you use this dataset, please cite:
@dataset{gupta_2020_pubmed_bioinformatics,
author = {Gupta, Yash M},
title = {PubMed Bioinformatics Abstracts (2020--2026)},
year = {2026},
publisher = {Hugging Face},
url = {https://huggingface.co/datasets/yashm/pubmed-bioinformatics-abstracts}
}
Please also cite the original data source:
Sayers EW, Bolton EE, Brister JR, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2022;50(D1):D13–D25. doi:10.1093/nar/gkab1112
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