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SODAR - the iRODS-powered System for Omics Data Access and Retrieval
Mikko Nieminen, Manuel Holtgrewe, Mathias Kuhring, and Dieter Beule
In the past years, a growing number of high-throughput omics assays in the areas of genomics, proteomics, and metabolomics have become widespread in life science research. This creates increasing demand for handling the large amounts of data as well as models for the complex experimental designs. Further challenges include the FAIR principles for making the data findable, accessible, interoperable, and reusable. Collaboration between multiple institutes further complicates data management.
Here we present SODAR (System for Omics Data Access and Retrieval), our effort of fulfilling these requirements. The modular system allows for the curation of complex studies with the required meta data as well as for the storage of large bulk data. To facilitate effective and efficient data management workflows, SODAR provides project-based access control, a web-based graphical user interface for data management, programmatic data access, ID management for study objects as well as various tools for omics data management.
The system is based on open source solutions. iRODS is used for large data storage while Davrods allows for providing access through the widely supported HTTP(S) protocol (e.g., for integration with the IGV software). Graphical interfaces and APIs are implemented in Python using the Django framework. Our data model is based on the ISA-Tools data model ISA-tab is used as the meta data file exchange format. A transaction sub system integrates activities spanning both data and meta data. Core parts of SODAR are available as reusable libraries for creating project-based data management systems that share access control with SODAR.
We will demonstrate our flag ship rare disease genetics use case, starting from bulk data import to the browsing of study design and metadata and interacting with the data through IGV.
Last modified: Jan 21, 2021