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Data stored in OmicsDM

OmicsDM was designed to store the following two data types:

  • 🧬 Omics Data

    Omics data is a high-throughput data type that is generated by technologies such as DNA/RNA-seq, proteomics, metabolomics etc.

    3TR specific

    Only submit processed data that is ready for analyses.

  • Pheno-Clinical Data

    Pheno-clinical (phenotypic + clinical) data is the data that describes the phenotype and clinical information of the samples from which the omics data was generated.

    In the best scenario, this data comes in the form of GA4GH standards such as:

    Phenopackets v2 or Beacon-friendly-format.

Omics Data Example

RNA-seq Data Example from CELLxGENE

In the python ecosystem one of the most used tool for single-cell RNA-seq data analysis is Scanpy, which is built on top of AnnData. The latter is a data structure for storing annotated data matrices, which can be saved to disk in the form of a .h5ad file.

Thus, you find below a .h5ad example, which not only can be stored in OmicsDM but also be explored using OmicsDM's visualisation module.

3TR specific

The visualisation module is disabled in the 3TR instance of OmicsDM.

Pheno-Clinical Data Example

Pheno-Clinical Information Exported from REDCap

In the 3TR project most of the Pheno-clinical information is stored in REDCap, a widely adopted web application for building and managing online surveys and database. The information is then exported in the form of two CSV files. Click on each link to see an example of the content of the files: