Metabolomics Publications in PubMed: Embeddings and Associated Datasets

File 1: pubmed_metabolomics_clean_01MAR2024.xml This is a cleaned-up XML file (entries with errors removed) for PubMed metabolomics-related publications covering the period from 1998 to early 2024. File 2: metabolomics_embeddings_full_tSNE_uMAP_01MAR2024.h5 This file contains the complete embeddings for metabolomics-related articles from PubMed and associated datasets, spanning from 1998 to early 2024. It includes: 1) PubMed data such as PMID, title, abstract, language, journal title, publication year, and authors. 2) The full 768-dimensional embeddings generated using PubMedBERT. 3) uMAP and t-SNE embeddings.