Omics Data Discovery Agents: Agent-Supported Retrieval, Reanalysis, and Synthesis of Published Omics Data

The biomedical literature contains a vast collection of omics studies, yet most published data remain functionally inaccessible for computational reuse.

When raw data are deposited in public repositories, essential information for reproducing reported results is dispersed across main text, supplementary files, and code repositories, and in the rarer cases where intermediate data (e.g. protein abundance files) are shared, their location is irregular.

Here we present an agentic framework for the agent-supported retrieval, reanalysis, and synthesis of published omics data.

The system employs large language model (LLM) agents with access to tools for fetching omics studies, extracting article metadata, identifying and downloading published data, executing containerized quantification pipelines, and synthesizing results across studies.

Applied at corpus scale, the pipeline cataloged dataset references across thousands of PubMed Central articles; we report these as descriptive system outputs rather than as a validated measure of extraction accuracy.

Using model context protocol (MCP) servers to expose containerized analysis tools, the agents retrieved and re-quantified data in five end-to-end reanalyses spanning data-dependent and data-independent proteomics and bulk RNA-seq.

All five reanalyses completed, each with documented human guidance and workflow accommodations, and reproduced the authors' deposited abundances with high per-sample correlation (0.85-0.997) and strongly concordant differentially expressed features (fold-change Spearman 0.88-0.91), with no direction reversals among features called differentially expressed in both analyses; residual differences in significant-feature lists were attributable to threshold placement, tool-version, and preprocessing differences rather than to the underlying quantities.