IMMEDIATE SODAR DMP system
Dive deeper into the SODAR DMP system with Hong Li (Max Delbrück Center) in our latest IMMEDIATE insight blog.
To simplify the complexities of data handling for the IMMEDIATE consortium, we are pursuing a modern data management platform (DMP) to ensure data security, integrity, and reusability between internal data cohorts as well as external partners. Existing software packages that fall into this category of DMP tools often provide similar functionalities in some specific research fields or various use cases. SODAR (System for Omics Data Access and Retrieval) - a suitable solution in life sciences has been developed since 2016 by the Core Unit Bioinformatics at the Berlin Institute of Health. This is an open-source software under MIT license, which avoids vendor lock-in and allows for maximum flexibility for IMMEDIATE project use case.
As an integrated system for managing omics-specific data and metadata, the SODAR DMP system uses the ISA (Investigation, Study, Assay) data model, which allows the user to model each processing step with each intermediate result and annotate each of these with arbitrary metadata. For data analysis, bioinformaticians and experimentalists access metadata in the sample sheets (in a web-based graphic user interface) as well as raw data in iRODS (Integrated Rule-Oriented Data System), the latter being linked to the former for ease of download access. In this case, all relevant data is kept in one place, with version control and backup. The data is under strict access controls, while it is also easily accessible for authenticated users. Thus, the FAIR principles are ensured in every data flow when using the IMMEDIATE SODAR DMP system.
Innovative AI Integration for Predictive Health Modeling
The IMMEDIATE SODAR DMP system has been set up by our data manager, who also works together with our bioinformaticians and experimentalists to validate the data structure and to ensure compatibility with general requirements and conventions. After creating the initial sample sheet templates for our common use cases, the researcher can easily fill in the metadata and upload it to the IMMEDIATE SODAR DMP system, which allows for easy search and modification in subsequent studies or investigations. Besides typical functions of the DMP, a more advanced feature under development in the framework of the IMMEDIATE project is to integrate the data management tool with the artificial intelligence (AI) platform, aiming for the power to predict the transition from health to disease at an individual level based on a large amount of data and studies.
Furthermore the IMMEDIATE SODAR DMP is modular and as such runs in a virtual machine. This allows deploying the same architecture on the hardware of other consortium members if this at some point is needed to ensure compliance with specific data transfer rules for datasets that may be under further restrictions, while still maintaining overall harmonization.