(Meta)data in Action - Developments in NFDI4BIOIMAGE and I3D:bio

(Meta)Data in Action Developments in NFDI4BIOIMAGE and I3D:bio Susanne Kunis With the exception of logos and cited third-party content, the content of these slides is shared under the terms of the Creative Commons Attribution License (CC-BY 4.0) unless the content is marked otherwise. 22.10.2025 Susanne Kunis RDM4mic Meeting STATUS: DATA SILO LEVEL: „If I want to share data, I coordinate it directly with my colleague” „My project/group has agree to use a specific platform for data management“ „ I should manage data and strive to use appropriate standards and tools.” „ I have learned how to apply data management policies and sharing has become much easier.” „ I find that I can easily discover, access, combine and publish data". highly individualized, flexible system - Structured - Collaborative - Rigorously documented - Institution-wide coordination & collaboration - Standardization - Accessibility - Security - Long-term preservation - Cross-institutional coordination & collaboration - Standardization & Interoperability - Significant investment in infrastructure & expertise - Strong leadership & a national vision for data-driven innovation. - Global data governance frameworks - Interoperable standards - Federated data networks - Data sharing agreements - Collaborative infrastructure local Centralized for working group Centralized local infrastructure National and domain specific infrastructure single use Resource to validate decisions Resource to make decisions Asset to answer future questionssingle use INDIVIDUAL 01 PROJECT/GROUP 02 INSTITUTIONAL 03 NATIONAL 04 INTERNATIONAL 05 DATA VALUE: Collaborative infrastructure Levels of Datamanagement 22.10.2025 Susanne Kunis RDM4mic Meeting STATUS: highly individualized, flexible system - Structured - Collaborative - Rigorously documented - Institution-wide coordination & collaboration - Standardization - Accessibility - Security - Long-term preservation - Cross-institutional coordination & collaboration - Standardization & Interoperability - Significant investment in infrastructure & expertise - Strong leadership & a national vision for data-driven innovation. - Global data governance frameworks - Interoperable standards - Federated data networks - Data sharing agreements - Collaborative infrastructure INDIVIDUAL 01 PROJECT/GROUP 02 INSTITUTIONAL 03 NATIONAL 04 INTERNATIONAL 05 Since 2019 2022-2025 2023-2028 Levels of Datamanagement 22.10.2025 Susanne Kunis RDM4mic Meeting I3D:bio Core Mission: Implement the needs of tools, support and training with focus on OMERO and light microscopy 4 GUIDE: Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data https://doi.org/10.5281/zenodo.7018928 Workshops & Training material Videos: https://tinyurl.com/mwykwj6h Slides: https://doi.org/10.5281/zenodo.8323587 Zenodo Community: https://zenodo.org/communities/i3dbio/records 22.10.2025 Susanne Kunis RDM4mic Meeting I3D:bio 5 https://doi.org/10.1111/jmi.13317 A practical guide to bioimaging research data management in core facilities An imaging-core-facility-centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community Includes tables of common issues and proposed solution for each stage in the live-cycle 22.10.2025 Susanne Kunis RDM4mic Meeting •omero-autotag, omero-tagsearch maintenance •OMERO.web inherit annotation from project/dataset •omero-linkage-toolbox: enables linking of bioimage metadata in OMERO with ELN (experimental metadata) •Gamification: “treasure hunt” about use of Tags and key-values in OMERO https://omero-training.gerbi-gmb.de/webclient/ •TiM data management concept and infrastructure •TiM OMERO server with public, annotated data: https://omero-tim.gerbi-gmb.de/webclient/ (kindly hosted by the NFDI4BIOIMAGE consortium) •Knowledge hub: https://gerbi-gmb.de/i3dbio/ I3D:bio what else… 6 22.10.2025 Susanne Kunis RDM4mic Meeting NFDI4BIOIMAGE Core Mission: Enable FAIR bioimage data management for German researchers,across disciplines and embedded in the international framework. 7 Maximum intensity projection in depth color coding of an optically cleared, one month old zebrafish, imaged in a light-sheet microscope. (Courtesy of J. Huisken and K. Weiss). The QR-code links to the image in an OMERO database. 22.10.2025 Susanne Kunis RDM4mic Meeting NFDI4BIOIMAGE FAIR Digital Objects for Bioimaging Cloud-ready open file formats Metadata standards & tools 8 Task Area 1: Image (meta)data formats & standardization 22.10.2025 Susanne Kunis RDM4mic Meeting 9 FDO-compatible datatype for bioimaging to ensure data is open and web-accessible to enable efficient distributed processing. FAIR Digital Objects for Bioimaging 22.10.2025 Susanne Kunis RDM4mic Meeting Large number of proprietary file formats (PFF): Many formats can only be read correctly with specific manufacturer software; otherwise, they need to be converted to widely accepted formats like TIF, which often results in the loss of metadata Diversity in formats 16 22.10.2025 Susanne Kunis RDM4mic Meeting Examples of Standards/Recommendations to describe technique or/and context: •OME Data model (Technical metadata description of an imaging experiment) •REMBI (Recommended Metadata for Biological Images) •4DN-BINA-OME-QUAREP (BNO) tiered metadata guidelines •3D-MMS (3D microscopy metadata standard) •BIDS (Brain Imaging Data Structure) for Microscopy •MITI (Minimum Information for Highly Multiplexed Tissue Images) •MIHCSME (Minimum Information for High Content Screening Microscopy Experiments) •MIFA (Metadata, Incentives, Formats and Accessibility guidelines for AI reuse) https://gerbi-gmb.de/2024/12/05/metadata-standards-for-bioimaging / Diversity in standards 17 22.10.2025 Susanne Kunis RDM4mic Meeting 18 - TIFF TIFF XML The model includes image parameters, such as XYZ dimensions and pixels type, as well as extensive metadata on, for example, image acquisition, annotation, and regions of interest (ROIs). Linkert, et al. (2010) Metadata matters: access to image data in the real world.The Journal of Cell Biology 189(5), 777-782. DOI: 10.1083/jcb.201004104 https://ome-model.readthedocs.io/en/stable/ome-tiff/specification.html 22.10.2025 Susanne Kunis RDM4mic Meeting Cannot represent all vendorspecific informations Not ideal to integrate “other” data 19 22.10.2025 Susanne Kunis RDM4mic Meeting Modular framework 20 Metadata standards & tools 22.10.2025 Susanne Kunis RDM4mic Meeting Metadata standards & tools Creating (meta)data representations is easy. The hard part is building a common one. 21 22.10.2025 Susanne Kunis RDM4mic Meeting . 22 Metadata standards & tools Improved data discovery: Semantic data integration enables the integration and harmonization of data from various bioimaging sources and related data. Increased data reuse: RDF facilitates linking and combining datasets for new insights. Enhanced interoperability: Data can be easily integrated and exchanged between different systems. Machine readability: Enables automated processing and analysis of metadata Goal: Web of metadata 22.10.2025 Susanne Kunis RDM4mic Meeting 23 Steps Conversion OMERO Data Model xsd -> LinkML to provide URIs for each Class and Predicate https://joshmoore.github.io/ome-ld/core/docs/Annotation.html Metadata standards & tools 22.10.2025 Susanne Kunis RDM4mic Meeting 24 Steps Translating OMERO-specific metadata into RDF via omero-rdf to obtain a semantically rich representation and simplify integration with data other domains $ omero rdf Image:165854 @prefix dcat: <http://www.w3.org/ns/dcat#> . @prefix dcterms: <http://purl.org/dc/terms/> . @prefix efo: <http://www.ebi.ac.uk/efo/> . @prefix fhir: <http://hl7.org/fhir/> . @prefix jerm: <http://jermontology.org/ontology/JERMOntology#> . @prefix obi: <http://purl.obolibrary.org/obo/OBI_> . @prefix ome: <http://www.openmicroscopy.org/Schemas/OME/2016-06#> . @prefix rocrate: <https://w3id.org/ro/crate/1.1/context> . @prefix sio: <http://semanticscience.org/resource/> . @prefix sioc: <http://rdfs.org/sioc/ns#> Metadata standards & tools 22.10.2025 Susanne Kunis RDM4mic Meeting 25 Steps Map OMERO metadata to Virtual Knowledge Graph via OMEROontop-mapping to act as a SPARQL endpoint to fetch data via SPARQL prefix omevol: https://evolomero.evolbio.mpg.de/rdf/ prefix image: https://evolomero.evolbio.mpg.de/rdf/Image/ prefix ds: https://evolomero.evolbio.mpg.de/rdf/Dataset/ prefix omecore: https://ld.openmicroscopy.org/core/ prefix rdfs: http://www.w3.org/2000/01/rdf-schema# prefix dc: http://purl.org/dc/elements/1.1/ prefix omekg: https://ld.openmicroscopy.org/omekg# select distinct ?img ?tag where { ?img a omecore:Image . values ?img {image:9} ?img omekg:tag_annotation_value ?tag } List all image tags: VKG Engine Metadata standards & tools