Medicine and Health
Research in support of healing by diagnosis, treatment, and prevention of disease.
See also: Medicine and Health in EDAM.
Related use cases
The Five Safes RO-Crate profile extend the Workflow Run RO-Crate profile for use in Trusted Research Environments (TRE).
Galaxy is a platform for FAIR data analysis which supports the building and execution of workflows. It can import and export RO-Crates for both regular datasets and workflow executions.
GIDE (Global Image Data Ecosystem) is a collaborative project working towards the interoperability of bioimage data repositories across the globe. The project was initially funded by a European Commission Horizon Grant as "foundingGIDE", including multiple partners from Europe, Australia and Japan. The GIDE project uses RO-Crates as a metadata exchange format to harmonize outputs from three major bioimaging repositories (SSBD, BioImage Archive and IDR).
LifeMonitor is a testing and monitoring service for computational workflows being developed as part of the EOSC-Life project. It aims to facilitate the execution, monitoring and sharing of workflow tests over time, allowing to detect deviations from expected workflow operation and provide useful feedback to the workflow authors
OME is a consortium producing open-source software and format standards for microscopy data. It uses RO-Crate as part of its system for transfering data between OMERO servers, as well as for producing self-documenting data in OME-Zarr, a next-generation file-format (NGFF) standard.
WfExS-backend is a high-level workflow execution command line program that consumes and creates RO-Crates, focusing on the interconnection of content-sensitive research infrastructures for handling sensitive human data analysis scenarios
The Semantic Technologies (SemTec) team in ZB MED uses GitHub pages to share research projects and corresponding research artefacts/outcomes.
Related tools
| Tool | Description | Status |
|---|---|---|
| 5s-crate-py | Python library to create and consume Five Safes RO-Crates for Trusted Research Environments, built on ro-crate-py | alpha |
| BioImage Archive (BIA) RO-Crate Validator | Data models for describing, parsing, and validating the RO-Crate profile for BioImage Archive (BIA). submissions, with supporting structures such as file lists. | |
| Common Data Model Builder (cdmb) | From a data model expressed in Python, generate a reproducible folder structure of the research project as a Research Object (RO). | |
| dsROCrate |
R package that wraps DataSHIELD federated analyses into Five Safes RO-Crates to track data access, project membership, analysis execution and output checking, with audit reports
|
beta |
| FiveSafes.Net | C# and .NET library for building Five Safes RO-Crates packaged as BagIt archives, built on ROCrates.Net | alpha |
| Galaxy |
Workflow system and web platform that exports Workflow RO-Crates and Workflow Run Crates of histories and invocations (from Galaxy 23.1.1)
|
production |
| HuBMAP data-containers |
Code for building and manipulating data containers like RO-Crate, Croissant, BagIt for HuBMAP
|
prototype |
| WfExS-backend |
Workflow Execution Service backend that runs Nextflow, CWL and Galaxy workflows reproducibly, including in Trusted Research Environments, and describes executions as Workflow Run Crates
|
beta |
See the tools and resources list for all RO-Crate tools.