A PubMed-Scale Dataset of Structured Biomedical Abstracts
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Computer Science > Information Retrieval
Title:A PubMed-Scale Dataset of Structured Biomedical Abstracts
Abstract:Structured abstracts are important for biomedical literature processing, by facilitating information retrieval, text mining, and knowledge synthesis. However, a vast portion of abstracts indexed in PubMed remain unstructured, presenting a significant bottleneck for downstream text-processing workflows and applications. To resolve this limitation, we introduce Structured PubMed, a comprehensive corpus of section-labeled biomedical abstracts compiled from the complete PubMed database, encompassing over 23.2 million research-article records. The corpus is divided into two distinct subsets: a collection of 5.9 million author-structured abstracts parsed from official XML files, and an automatically labeled collection of 17.2 million originally unstructured abstracts structured via a verbatim-extraction Large Language Model pipeline. Every record is harmonized under a unified five-section schema and mapped to its original PubMed identifier, publication type, and publication date. This dataset can be utilized to train sentence-classification models, benchmark text-segmentation architectures, and perform large-scale, section-specific information extraction at an unprecedented PubMed-wide scale.
| Comments: | Data and code for this work are available at this https URL and this https URL, respectively |
| Subjects: | Information Retrieval (cs.IR); Computation and Language (cs.CL) |
| Cite as: | arXiv:2606.11361 [cs.IR] |
| (or arXiv:2606.11361v1 [cs.IR] for this version) | |
| https://doi.org/10.48550/arXiv.2606.11361
arXiv-issued DOI via DataCite (pending registration)
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Submission history
From: Chia-Hsuan Chang Dr. [view email][v1] Tue, 9 Jun 2026 18:42:20 UTC (911 KB)
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