Data from the paper "The landscape of biomedical research"

<p>Data from the paper "<a href="https://www.cell.com/patterns/fulltext/S2666-3899(24)00076-X">The landscape of biomedical research</a>".</p> <p>The paper used the PubMed 2020 baseline (download date: 26.01.2021, not available anymore) supplemented with additional files from the 2021 baseline (download date: 27.04.2022, not available anymore), both originally obtained from <a href="https://www.nlm.nih.gov/databases/download/pubmed_medline.html">https://www.nlm.nih.gov/databases/download/pubmed_medline.html</a>, courtesy of the U.S. National Library of Medicine. This data can be found in v2 of this repository (<a href="../records/7849020">https://zenodo.org/records/7849020</a>).</p> <p>In the latest version of this repository we provide the PubMed 2024 baseline (download date: 06.02.2024) including all papers until the end of 2023, which is&nbsp;<strong>not</strong> the main data we analyzed in the paper but an updated version including newer articles. The paper contains two supplementary figures (S9 and S10) with the updated embedding.</p> <p>The latest version provided here includes the following files:</p> <p>pubmed_landscape_data_2024_v2.zip, which includes:</p> <p>- from the PubMed database: article title, journal, PMID, and publication year.</p> <p>- produced by us: t-SNE embedding X and Y coordinates, label, color, whether the paper is retracted or not (combining PubMed and Retraction Watch information), affiliation country ( from the first affiliation of the first author), and inferred gender (of both first and last author).</p> <p>(Note: pubmed_landscape_data_2024_v2.zip is identical to pubmed_landscape_data_2024.zip from v3 of this repository, but includes inferred genders additionally.)</p> <p>&nbsp;</p> <p>pubmed_landscape_abstracts_2024.zip, which includes:</p> <p>- from the PubMed database: PMID, and paper abstracts.</p> <p>&nbsp;</p> <p>PubMedBERT_embeddings_float16_2024.npy, which includes:</p> <p>- produced by us: PubMedBERT embeddings of the paper abstracts (numpy.ndarray of shape&nbsp;23,389,083x768).</p>