Glossary
- Application
In SODAR, a group of views and actions related to a specific functionality are called an application, or app for short. In the SODAR UI, applications can be recognized by their links in the project sidebar or the user dropdown, as well as URL patterns. Applications can either be project specific or site-wide applications. The most prominent applications in SODAR are Sample Sheets, Landing Zones, and the Timeline.
- Assay
In the context of SODAR, assay refers to assays as defined in the ISA-Tab specification. For more information, see Metadata Recording.
- Assay Plugin
SODAR internally uses assay plugins to determine how assay shortcuts and links to iRODS data are determined and presented to the user. For more information see Advanced Metadata Topics.
- HPO
- IGV
- Investigation
Investigation is the topmost structure in the ISA-Tab format. An investigation can contain one or more studies. SODAR supports one investigation per project. For more information, see Metadata Recording.
- iRODS
- ISA-Tab
The TSV-based file format for the ISA Framework specification.
- JSON
JavaScript Object Notation, the format used for providing data in e.g. sample sheet editing.
- Landing Zone
User-specific file area with write access. Used for uploading files which will then be transferred into the read-only sample data repository.
- Markdown
Lightweight text-to-HTML markup language for creating formatted text. Used in e.g. project ReadMe documents.
- REST API
An application programming interface following the representational state transfer (REST) principles.
- Sample Data Repository
Read-only file area containing the sample and study data files accessible through sample sheets. Files are uploaded here through landing zones.
- Sample Sheets
Project study design and sample metadata, presented in a tabular form and grouped into studies and assays. Based on the ISA Framework and enhanced with SODAR-specific links, shortucts and additional features.
- SODAR
System for Omics Data Access and Retrieval.
- Study
In the context of SODAR, study refers to studies as defined in the ISA-Tab specification. For more information, see Metadata Recording.
- TSV
Tab-separated Values. A data format used e.g. by the ISA-Tab specification.
- UUID
Universally unique identifier. Used in SODAR to refer to all relevant objects in the system.
- WebDAV
Web Distributed Authoring and Versioning. Used in SODAR to provide web-based access to files, mount iRODS collections as network drives, provide random access to large files and link files to external tools such as IGV.