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

Sisi Deng
2026 · doi:10.5281/zenodo.19185349 · W7140105664
other OA: green CC0
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This Zenodo package provides the scripts, environment metadata, and analytical artifacts necessary to reproduce serum metabolomics-based endometriosis modeling workflows, including nested cross-validation and mechanistic profiling.

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This submission provides a reproducibility package for a study on serum metabolomics-based endometriosis modeling and exploratory mechanistic profiling. The archive contains R scripts, environment metadata, execution notes, and summary-level analytical artifacts necessary to replicate the workflow described in the associated BMC Medicine manuscript. It details methods such as nested cross-validation, temporal validation, and age or BMI-matched sensitivity analyses while explicitly excluding participant-level raw data due to ethical and custodial restrictions. This paper is centrally about endometriosis — specifically involving serum metabolomics modeling to identify potential mechanistic profiles associated with the disease.

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Abstract

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.
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Manuscript reproducibility package for serum metabolomics-based endometriosis modelling and exploratory mechanistic profiling Description 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. Files manuscript_repro_package_v1.zip Files (146.4 kB) | Name | Size | Download all | |---|---|---| | md5:5e2b8eef214847bfe95198109667a29a | 146.4 kB | Preview Download | Additional details Funding Dates - Created - 2026-03-23 Software - Programming language - R

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endometriosis

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last seen: 2026-06-22T06:09:18.325942+00:00
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