MOD-Finder: Identify multi-omics data sets related to defined chemical exposure

TL;DR

MOD-Finder is an automated tool that efficiently searches multiple public databases for multi-omics datasets related to specific chemical exposures, simplifying the process of integrating diverse biological data layers.

Contribution

It introduces an R-based web application that automates the retrieval and presentation of multi-omics data linked to chemical exposures across various repositories.

Findings

Automated search reduces manual effort in data collection.

Integrates data from multiple omics layers and repositories.

Provides effect information associated with chemicals of interest.

Abstract

Summary: Integration of multi-omics data on chemical exposure of cells or organisms promises a more complete representation of the responding pathways than single omics data. Data of different omics layers, like transcriptome or proteome is deposited in different repositories. Additionally, precisely specifying a chemical of interest that was used in the exposure experiments suffers from different nomenclatures and non-uniquely mapping of chemical identifiers. The manual search for corresponding omics data sets of different layers for exposure with a chemical of interest is thus a tedious task. We have developed MOD-Finder (Multi-Omics Data set Finder) to efficiently search for chemical-related omics data sets in several publicly available databases in an automated manner. A plain and simple presentation of the returned omics data sets is augmented with effect information that are assumed to be triggered by the chemical of interest. Availability and Implementation: MOD-Finder is implemented in R using the Shiny package. The web service is available at https://webapp.ufz.de/mod_finder and the source code under the GNU GPL v3 license at https://github.com/yigbt/MOD-Finder. Supplementary information: Supplementary data are available at https://www.ufz.de/index.php?en=44919