DOI: 10.5281/zenodo.17229455
title: Curated Biomedical Abstracts Dataset - Provenance-Verified, Deduplicated, Refined Labels (v1.0)

description: Title: Biomedical Abstracts Corpus — Provenance-Verified, Deduplicated, Refined Labels (v1.0)

DOI: 10.5281/zenodo.17229456

Date created: 2025-09-29

Creators: Idris Babalola, Adewale Alex Adegoke, Peter Adebayo Odesola

Contact: eidreiz01@gmail.com

====================================Dataset overviewThis deposit provides a curated biomedical abstracts corpus derived from a widely used Kaggle community dataset. The aim is a reusable, provenance-verified resource for text-classification tasks across major disease areas (e.g., cardiovascular, digestive system, neoplasms, nervous system). 

====================================

Scope & counts

Total records in source: 14,438

Duplicates/near-duplicates removed: 6,140

Additional filtering: removed “General Pathological Conditions” class and short abstracts (length-based threshold)

Final unique records: 5,901

Final label set: Cardiovascular Diseases, Digestive System Diseases, Neoplasms, Nervous System Diseases

====================================Provenance verification (PubMed spot-check)A random sample of records was cross-referenced against PubMed. 99/100 sampled records returned PMIDs, supporting source traceability and dataset credibility. (See docs pubmed_spotcheck_results.csv included.)

Note: Code is archived separately and will also be made available on GitHub soon.

====================================

Methods 

Deduplication: combined text-similarity and metadata to remove duplicates.

Label design: normalized disease labels and retired the broad “General Pathological Conditions” class after six diagnostics checks(e.g i. lexical overlap, ii. unsupervised separability based on TF-IDF(1-2) class centroids, iii. intra-class cohesion, distinctiveness estimated via log-odds with an informative Dirichlet prior), to reduce semantic bleed-over that hindered class separability.

Short-abstract filter: removed entries below a minimum length threshold to improve training quality.

Provenance: PubMed ID recovery via title/metadata matching; PMIDs recorded where found.

====================================Intended use

Biomedical NLP: supervised/unsupervised text classification, benchmarking, Reliability & Model uncertainty, LLM use case.

Curation & reproducibility: exemplars for deduplication, provenance checks, and label-taxonomy repair.

====================================Licensing

This derived dataset (metadata, labels, keys): CC BY-SA 3.0.

Original dataset license: CC BY-SA 3.0 (see https://github.com/sebischair/Medical-Abstracts-TC-Corpus & https://huggingface.co/datasets/TimSchopf/medical_abstracts).

Redistribution is permitted under ShareAlike terms; please attribute both the original creators and this curated release.

Abstract text itself may be subject to third-party rights. Users should respect source terms when retrieving full text.

====================================Funding & competing interestsThis work received no funding. The authors declare no conflicts of interest. The curation and validation were conducted independently and are not endorsed by our current or past affiliations.

====================================

Acknowledgments & original sourceThis corpus is derived from the original community dataset created by https://www.kaggle.com/datasets/chaitanyakck/medical-text. We thank the original creators for making their resource available under CC BY-SA 3.0.