SODAR stands for the System for Omics Data Access and Retrieval. It is a centralized system for providing access to raw data, results, and metadata in omics research projects. SODAR is targeted for researchers and project owners who want to manage their experiment data according to the FAIR principles: findable, accessible, interoperable and reusable.
SODAR aims at providing the following capabilities for managing omics research data:
Project based access control and data encapsulation
Modeling and management of study design metadata
Large scale data storage
Linking files to metadata
Management and validation of file uploads
Tools for aiding project data management
Integrating data with third party tools
The SODAR data workflow involves the following elements:
- Projects and Categories
In SODAR, data and user access are structured into projects, which exist under categories. Projects contain project study modeling, file data and other project related functionality. A category can be thought of as a project with no data and the possibility to contain other categories or projects under it.
- Sample Sheets
Sample sheets contain the sample, process and material metadata for project studies. They are modeled in the ISA Model standard as investigations, studies and assays. One SODAR project can contain one investigation with one or more studies.
- Large Scale Data Storage
The actual sample data files for studies and assays are stored in a distributed file system built on iRODS. This data can contain anything from binary alignment map files to e.g. reports and log files. The files can be accessed through relevant sample sheet metadata in SODAR.
- Landing Zones
Uploading new sample data is done through landing zones, which are temporary user-specific file areas with write access. Once uploads are prepared, SODAR validates the files and moves them into the read-only sample data repository.
User access via one or multiple LDAP/AD services, Single Sign-On via SAML and/or local accounts
Access tokens can be can be generated for REST API use
UUIDs and permanent URLs for all relevant objects in the system
- iRODS Integration
Automated iRODS environment file generation
WebDAV for mounting iRODS as a network drive and web-based browsing of files, supporting random file access
- Sample Sheets
Sample sheet import from existing ISA-Tab TSV files
Sample sheet generation from templates
Sample sheet editing and version control
Sample sheet export in ISA-Tab and Excel formats
Automated iRODS shortcut generation for e.g. BAM/VCF files
Automated Integrative Genomics Viewer (IGV) session file generation and merging
Track hub management for UCSC Genome Browser integration
- Landing Zones
Automated validation and of file uploads
Transactions with rollback for file transfers to avoid invalid or incomplete data to be entered to projects
Automated generation of expected iRODS collections for standardized data structures
- Other Features
Searching for sources, samples and files in iRODS
Timeline application for enhanced event logging an providing audit trails