ARC Tools and Services

An end-to-end GUI application to manage ARCs. The ARCitect bundles many of the individual tools from DataPLANT into a single GUI application. Create and edit your ARCs. Synchronize ARCs with the PLANTdataHUB. Use Swate to enrich Assays and Studies with metadata from ontologies. Edit any metadata directly. 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 ISArchives through BrAPI. MIRA is a tool that allows the deployment of a Breeding API (BrAPI) server on top of an ARC containing phenotyping information compliant to the Minimal Information About a Plant Phenotyping Experiment (MIAPPE) standard. The tool can be deployed on a release of an ARC and uses the well-defined structure of the ARC to automate the population of the endpoints.

The brapi2arc API allows researchers to submit phenotyping observations to a dataset stored as an Annotated Research Context (ARC) through the Breeding API (BrAPI). BrAPI provides a standardized interface for sharing plant breeding data across applications enabling the integration of external tools in the user’s ARC workflow.

Reference implementation of the ARC Data Hub concept as a collaborative cloud repository for ARCs based on GitLab.Contains 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 familiar, spreadsheet-like work environment that makes it easy to incrementally increase metadata quality of an ARC Scaffold. 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 ARC Scaffold directory structure with the necessary root directories, and provides commands to manipulate 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 CLI-based tool to export different ARC metadata representation formats.

A uniform, polyglot (.NET, Python, Javascript), low-level library for creating and managing ARCs. The ARCtrl library supports a wide set of base operations for working with different ARC representations, which it can parse and write. 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.