ARC Tools and Services

A graphical application for managing ISA-based ARC workspaces. ARCitect brings together tools from DataPLANT in a single interface. Create and edit your workspace. Synchronize ARCs with the PLANTdataHUB. Use Swate to enrich Assays and Studies with metadata from ontologies. Edit the supported metadata through the application. Select validation packages to use in ARC Data Hub CQC pipelines.

Biologist-friendly application for creating MIAPPE-compliant metadata. The MIAPPE Wizard provides a convenient interface for users to generate metadata compliant with configurable metadata checklists, such as the Minimal Information About a Plant Phenotyping Experiment (MIAPPE) standard. The tool facilitates the direct upload of the new dataset as an ARC to the PLANTDataHUB.

Enabling access to MIAPPE-compliant ISA-based datasets through BrAPI. MIRA supports deployment of a Breeding API (BrAPI) server for an ISA-based ARC workspace containing phenotyping information compliant with the Minimal Information About a Plant Phenotyping Experiment (MIAPPE) standard. It uses the supported workspace structure and metadata to populate the endpoints. These are conventions of that implementation, rather than requirements of every ARC workspace.

The brapi2arc API allows researchers to submit phenotyping observations to an ISA-based ARC workspace through the Breeding API (BrAPI). BrAPI provides a standardized interface for sharing plant breeding data across applications, supporting integration with the user’s research workflow.

An established implementation of the ARC Data Hub concept, providing collaborative Git-based ARC workspaces through GitLab. It includes self-hosting and federation options. Implements CQC pipelines for ARC validation distributed via the AVPR service, and a semi-automated data publication process for the ARChive based on CQC hooks. The ARC Search service can be used to search for ARCs across federated instances.

Swate is a tool for ontology-driven metadata annotation. It provides a spreadsheet-like work environment for maintaining tabular annotations in an ISA ARC Workspace. Swate is integrated into the ARCitect, but can also be used as a standalone-web based tool.

An intermediate ontology that acts as a broker and bridge between the individual researcher/domain experts and main ontology providers.

A central registry for custom ARC validation packages hosted by DataPLANT. Can be used to browse available packages, their metadata, and validation code. Also offers API endpoints to retrieve validation packages programmatically.

ARC metadata search across all federated DataHUB instances.

A data publication repository for ARCs with integrated DOI minting.

A CLI-based tool to create, manage and share your ARCs. The major function of the ARC Commander is to set up the ARC directory and put it under version-control for you. It creates the established ISA-based workspace directory structure and provides commands to manipulate supported metadata. Useful for cases where ARCs need to be manipulated in bulk, but a full-blown programming environment is not necessary, e.g. for shell scripting.

A CLI-based tool to install, manage, and execute ARC validation packages. arc-validate is used to run ARC validation in CQC pipelines at PLANTdataHUB.

A command-line tool for exporting supported ARC metadata representations. Available formats and mappings depend on the tool version; generating metadata is separate from depositing an output with a publication service.

A polyglot (.NET, Python, Javascript) library for working with established ARC workspace and metadata formats. ARCtrl provides parsing, writing, and manipulation operations for supported ARC representations. Format and profile support depend on the library version. It supports all sorts of CRUD operations on the top-level layer, including manipulation of investigations, studies, assays, persons and many more. You can read more about the ARCtrl developer toolkit here.