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yashm/pubmed-bioinformatics-abstracts_all_years

PubMed Bioinformatics Abstracts — All Years A curated dataset of bioinformatics research abstracts fetched from PubMed via the NCBI Entrez API, covering publications from 1990 through 2026. Designed for LLM fine-tuning, biomedical NLP, and scientific text analysis. Curated by: Dr. Yash M Gupta Pipeline: yashmgupta/pubmed-bioinformatics-abstracts Intended Use Fine-tuning large language models (LLMs) on biomedical / bioinformatics domain text. Data… See the full description on the dataset page: https://huggingface.co/datasets/yashm/pubmed-bioinformatics-abstracts_all_years.

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PubMed Bioinformatics Abstracts — All Years

A curated dataset of bioinformatics research abstracts fetched from PubMed via the NCBI Entrez API, covering publications from 1990 through 2026. Designed for LLM fine-tuning, biomedical NLP, and scientific text analysis.

Curated by: Dr. Yash M Gupta Pipeline: yashmgupta/pubmed-bioinformatics-abstracts

Intended Use

Fine-tuning large language models (LLMs) on biomedical / bioinformatics domain text.

Data Fields

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

Only articles with non-empty abstracts are included.

Collection Method

—Source: NCBI PubMed via Entrez E-utilities (Biopython)
—Query: bioinformatics[MeSH Terms] AND hasabstract[text] AND journal article[pt]
—Date range: 2017–2019 (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:

bibtex

@dataset{gupta_2026_pubmed_bioinformatics_all_years,
  author       = {Gupta, Yash M},
  title        = {PubMed Bioinformatics Abstracts -- All Years},
  year         = {2026},
  publisher    = {Hugging Face},
  url          = {https://huggingface.co/datasets/yashm/pubmed-bioinformatics-abstracts_all_years}
}

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