Manuscript reproducibility package for serum metabolomics-based endometriosis modelling and exploratory mechanistic profiling

This Zenodo record contains the manuscript-focused reproducibility package prepared for the revised BMC Medicine submission on serum metabolomics-based endometriosis modelling and exploratory mechanistic profiling. It includes the scripts, environment metadata, execution notes, random seeds, and summary-level frozen analytical artefacts required to document and reproduce the reported workflow from authorized harmonized input tables. The package covers nested cross-validation model development, temporal validation, age/BMI-matched sensitivity analysis, exploratory mechanistic modelling, and figure-generation scripts for the main and supplementary displays. It also includes environment information, package-version records, and a manifest with checksums. This public deposit does not include participant-level raw data, participant-level prediction outputs, matched participant-level annotated tables, identifier-linkage files, collaborator transfer documents, or manuscript-assembly utilities. Access to participant-level cohort data remains controlled by the relevant custodians and is subject to local approvals, ethics restrictions, and transfer agreements.