Glossary¶

This glossary defines key terms used throughout the CropXR documentation.

Platforms and Services¶

Term	Definition
Resilience Hub	The CropXR platform for sharing research data, provided by DataXR. It combines the metadata catalogue with data storage, and will be extended with services such as compute and pipelines. See Resilience Hub.
Research Drive	The previous storage platform for research data within CropXR, hosted by SURF. It is no longer used for new data, but existing data remains available. See Research Drive.
rhub	The command line tool for uploading data to and downloading data from the Resilience Hub. See Command Line Tool.
Catalogue	A searchable registry where researchers can find studies, models and pipelines within the consortium. The catalogue is built on FairdomSEEK.
FairdomSEEK	The open-source platform used for the CropXR metadata catalogue. It implements the ISA framework for organizing research data. See SEEK Metadata Entry.
SharePoint	A shared document repository for policies, procedures, and administrative information within CropXR.
DataXR	The data management team within CropXR responsible for data infrastructure, support, and tooling.

Term	Definition
ISA	Investigation-Study-Assay. A general-purpose framework for structuring experimental metadata. ISA organizes research into three hierarchical levels: Investigations (research themes), Studies (specific experiments), and Assays (measurements). See the ISA specification.
MIAPPE	Minimum Information About Plant Phenotyping Experiments. A metadata standard for plant phenotyping experiments. CropXR uses MIAPPE in combination with ISA for phenotyping studies.
ENA	European Nucleotide Archive. A repository and metadata standard for nucleotide sequencing data. CropXR uses ENA standards in combination with ISA for sequencing studies.

Term	Definition
Investigation	The top level of the ISA hierarchy. An investigation represents a broader research theme, typically encompassing the work of a PI or multiple researchers. An investigation contains one or more studies.
Study	A collection of related experiments that together address a research question, roughly equivalent in scope to a publication. A study contains assays and is part of an investigation. See Defining a Study.
Assay	A measurement or analytical process performed on samples. In FairdomSEEK, multiple processing steps can be chained together in an assay stream.
Assay Stream	A sequence of connected assays in FairdomSEEK, representing a workflow from sample to data output.
Source	The starting biological material in a study, such as a plant variety under specific growth conditions. Sources are used to define experimental groups and conditions.
Sample	Material derived from a source, such as a tissue sample taken from a plant. Samples serve as inputs to assays.
Observation Unit	The entity on which measurements are performed. This can be at various levels: individual plant, plot, greenhouse, etc. The level determines the granularity of the associated data.

Term	Definition
Consortium Agreement	The legal document governing collaboration, intellectual property, and data sharing within the CropXR consortium.
Data Access and Deposit Manual	A document specifying data sharing policies for the consortium, internally as well as externally, available on SharePoint. See Policies and Data Sensitivity Levels.
MMP	Metadata Management Procedure. The SharePoint documentation describing the process of study setup, data upload, and metadata management.
SOP	Standard Operating Procedure. A documented protocol describing how an experimental or analytical procedure is performed. SOPs can be linked to studies and assays in the catalogue.