# SmilODB: a multi-omics database for the medicinal plant danshen (Salvia miltiorrhiza, Lamiaceae)

## TL;DR

SmilODB is a new database that combines genomic, transcriptomic, proteomic, and metabolomic data for the medicinal plant Danshen, helping researchers study its molecular mechanisms and therapeutic uses.

## Contribution

The novel contribution is the creation of an integrated multi-omics database for Salvia miltiorrhiza, unifying diverse data types and providing predictive protein structures.

## Key findings

- SmilODB includes two genome assemblies and 48 tissue-specific transcriptome datasets.
- The database provides 2,967 high-confidence protein models predicted using RoseTTAFold.
- It integrates biosynthetic pathways for key bioactive compounds like tanshinones and salvianolic acids.

## Abstract

Salvia miltiorrhiza Bunge (Danshen) is a traditional medicinal plant widely used in the treatment of cardiovascular and inflammatory diseases. Although various omics resources have been published, there remains a lack of an integrated platform to unify genomic, transcriptomic, proteomic, and metabolomic data.

To address this gap, we constructed the S. miltiorrhiza Multi-omics Database (SmilODB, http://www.isage.top:56789/), which systematically integrates publicly available genome assemblies, transcriptome datasets, metabolic pathway annotations, and protein structural predictions. Protein structures were predicted using the RoseTTAFold algorithm, and all data were visualized using interactive heat maps, line charts, and histograms.

SmilODB includes: (i) two genome assemblies of S. miltiorrhiza, (ii) 48 tissue-specific transcriptome datasets from root, leaf, and other vegetative tissues, (iii) annotated biosynthetic pathways for bioactive compounds such as tanshinones and salvianolic acids, and (iv) 2,967 high-confidence protein models. The database also integrates bioinformatics tools such as genome browsers, BLAST, and gene heatmap generators.

SmilODB provides an accessible and comprehensive platform to explore multi-omics data related to S. miltiorrhiza. It serves as a valuable resource for both basic and applied research, facilitating advances in the understanding of this medicinal plant’s molecular mechanisms and therapeutic potential.