With the availability of numerous Research Data Management (RDM) tools and platforms, a promising aspect emerges: the potential for enhanced data integration through improved format interoperability and comprehensive metadata.
Many members of the newly funded NFDI4BIOIMAGE consortium use OMERO (Open Microscopy Environment Remote Objects) as one of the tools supporting the RDM-compliant research data lifecycle for microscopy and bio-image analysis. OMERO is a data management platform for microscopy (meta)data that allows users to view, organize, analyze and share data. OMERO has many features and expansion points to integrate with other existing tools.
The ARC (Annotated Research Context) will be explored for OMERO with a focus on metadata interoperability. ARCs provide a hierarchical, feature-rich directory structure adhering to various standards. While originally being developed for plant biological research by the DataPLANT consortium, ARCs offer the extensibility necessary for interoperability with the bio-imaging domain across disciplines. ARCs are designed to serve as FAIR Digital Objects (FDOs) in which data can be stored and processed along with its metadata. They are based on ISA, CWL and RO-Crate, enable version control, collaboration, and are supported by several tailor-made DataPLANT tools.
Our goal is to enable integration of ARC-like data structures with OMERO. We want to focus on the following main areas:
- Conceptual part: Developing templates that can seamlessly integrate with various research areas and imaging modalities within OMERO and ARCs. This involves designing efficient methods for transferring metadata accompanying image data stored in both ARCs and OMERO. [beneficial skills: OMERO, ARC]
- Data curation: Existing ARCs containing microscopy data are transferred to OMERO and vice versa. Participants can work on their own datasets or use existing examples. This will validate the conceptual part and prepare the technical part. [beneficial skills: OMERO or ARC, image data]
- Technical implementation: Enable import/export of meta(data) from and to specialized and domain-specific data management solutions, such as OMERO.[beneficial skills: Programming, e.g. Python, Java]
Expected outcomes:
- A roadmap of required steps to map the two specifications.
- Functional metadata templates to conveniently annotate data in OMERO and ARC enabling interconversion.
- Transfer of exemplary data from different disciplines between ARC and OMERO.
- Initiate tool development for automatic exchange of (meta)data and required validation procedures.
- Connecting ARC and OMERO experts
Our long-term goal is to develop a (conceptual and technical) framework that supports the interoperability of imaging data and facilitates the integration of data in OMERO with external (multi-)omics data structures and repositories.
By bringing together ARC and OMERO experts and practitioners, the 2nd BioHackathon Germany provides a great opportunity for cross-consortium exploration of FAIR integration with participants from data management, bioinformatics and other fields. This will help in improving the interoperability of image (meta)data from biology, medicine and plant sciences in general.
Project lead: 1) Niraj Kandpal, University of Cologne (