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MethylCurate: Tool for Dataset Curation and Epigenetic Aging Clock Evaluation.

Travyse A Edwards¹, Qi Long¹, Li Shen¹

¹University of Pennsylvania, Philadelphia, PA, United States.

Biorxiv : the Preprint Server for Biology

|May 25, 2026

Summary

MethylCurate automates DNA methylation dataset retrieval and metadata harmonization from the Gene Expression Omnibus (GEO). This AI framework streamlines epigenetic aging clock evaluation by standardizing data and improving accessibility.

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Area of Science:

Epigenetics and computational biology.
Bioinformatics and data science.

Background:

Public DNA methylation datasets are crucial for epigenetic aging clock development.
Existing tools face challenges in dataset retrieval and metadata harmonization from repositories like NCBI Gene Expression Omnibus (GEO).
Inconsistent data structures and manual interventions hinder scalable clock evaluation.

Purpose of the Study:

To develop an automated framework, MethylCurate, for efficient DNA methylation dataset processing.
To address bottlenecks in dataset retrieval, metadata harmonization, and clock evaluation.
To enable scalable and standardized benchmarking of epigenetic aging clocks.

Main Methods:

Developed MethylCurate, an agentic AI framework using Python.
Combined deterministic modules with large language model-assisted agents.

Keywords:

Biological age Biomarkers of Aging DNA methylation Epigenetic aging clocks Longevity

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Automated dataset retrieval, quality control, metadata extraction, harmonization, and data parsing from GEO.

Main Results:

MethylCurate automates the retrieval and harmonization of DNA methylation datasets from GEO.
The framework standardizes heterogeneous metadata and maps datasets to a unified format.
Enables integrated and dialogue-driven workflow for scalable epigenetic aging clock evaluation.

Conclusions:

MethylCurate overcomes limitations of existing resources for DNA methylation data.
Facilitates streamlined and automated preprocessing and metadata harmonization.
Provides a scalable platform for benchmarking epigenetic aging clocks.