=Paper=
{{Paper
|id=Vol-3890/paper-40
|storemode=property
|title=There and back again: RDF as a bridge to domain-platforms like OMERO
|pdfUrl=https://ceur-ws.org/Vol-3890/paper-40.pdf
|volume=Vol-3890
}}
==There and back again: RDF as a bridge to domain-platforms like OMERO==
https://ceur-ws.org/Vol-3890/paper-40.pdf
There and back again: RDF as a bridge to
domain-platforms like OMERO
Josh Moore1,† , Andra Waagmeester2,† , Kristina Hettne3 , Katherine Wolstencroft4 and
Susanne Kunis5
1
German BioImaging e.V, Society for Microscopy and Image Analysis, Konstanz, Germany
2
Micelio, Belgium
3
Centre for Digital Scholarship, Leiden University Libraries, The Netherlands
4
Leiden Institute of Advanced Computer Science, The Netherlands
5
Department of Biology/Chemistry and Center for Cellular Nanoanalytics, University Osnabrück, Germany
Keywords
Open Microscopy Environment (OME), Bioimaging, Resource Description Framework (RDF)
The production of digital images in biomedical research is a field in rapid evolution, with 500
newly indexed articles on PubMed each day in the life-sciences alone[1]. The ever-increasing
volume of bioimages and the granularity of metadata and annotations complicate data man-
agement. OMERO[2] is an open-source platform built to manage information from the over
160 bioimaging file formats[3] produced by microscopes using the Open Microscopy Environ-
ment (OME) data model[4]. Beginning in 2005, the history of OMERO reflects the evolution of
bioimaging, adapting to the growing complexity of data. Interestingly, OMERO’s development
predates the formalization of FAIR[5] principles and even the widespread use of JSON. An
early attempt was made to base OMERO on RDF, but just a year after the 1.0 release of RDF,
performance considerations led to the development of a more traditional SQL approach. Grow-
ing demands for annotations, though, have led OMERO to incorporate a system of structured
annotations, weaker than the expressivity of RDF but still based on the same concepts.
While users of OMERO are appreciative of the ability to manage, annotate, and critically
view their images, they must also link these results into wider FAIR management platforms.
Generic RDM tools like iRODS and RO-Crate[6] exactly allow researchers to link disparate
products of their investigations, aiding accessibility and interoperability. Other platforms like
Fair Data Points[7] (FDP) improve the findability of datasets. In each of these cases, a domain-
agnostic representation of OME data is needed to make images FAIR. Even within the life
sciences, more general models such as the Investigation-Study-Assay model[8] (ISA) require
mapping out of the conceptual bioimaging space. This is of interest for national level research
SWAT4HCLS 2024: Semantic Web Applications and Tools for Health Care and Life Sciences, Feb 26–29, 2024, Leiden, The
Netherlands
†
These authors contributed equally.
Envelope-Open josh@openmicroscopy.org (J. Moore); andra@micel.io (A. Waagmeester); k.m.hettne@library.leidenuniv.nl
(K. Hettne); k.j.wolstencroft@liacs.leidenuniv.nl (K. Wolstencroft); sukunis@uos.de (S. Kunis)
Orcid 0000-0003-4028-811X (J. Moore); 0000-0001-9773-4008 (A. Waagmeester); 0000-0002-4182-7560 (K. Hettne);
0000-0002-1279-5133 (K. Wolstencroft); 0000-0001-6523-7496 (S. Kunis)
© 2024 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
CEUR
Workshop
Proceedings
http://ceur-ws.org
ISSN 1613-0073
CEUR Workshop Proceedings (CEUR-WS.org)
projects such as DataPlant within Germany’s National Research Data Infrastructure (NFDI)
with their Annotated Research Context[9] (ARC) as well as the Dutch FAIR Cell Observatory, a
high content screening project in the Netherlands Bioimaging network with their Minimum
Information for High Content Screening Microscopy Experiments[10] (MIHCSME) which in
turn is based on the REMBI minimum information model[11]. Work with patient data has also
shown that an intermediary is needed to bridge OMERO data with the highly tabular world of
patient records. Whether dedicated platforms such as RedCap[12] or custom spreadsheets, the
domain-specific model should and really cannot be extended to encompass the many existing
biomedical ontologies that exist today. Instead, they must be made to work together.
In these use cases, RDF emerges as the most robust mechanism for capturing the complexity
and diversity of metadata in bioimaging. To this end, we are currently developing omero-rdf[13]
to provide consistent bridging between the domain-specific and agnostic worlds. From there,
we will explore higher-level frameworks such as LinkML, YARRML, and ShExML frameworks
for data modeling and transformation.
References
[1] C. Schmied, H. K. Jambor, Effective image visualization for publications - a workflow using
open access tools and concepts, F1000Res. 9 (2020) 1373.
[2] C. Allan, et al., OMERO: flexible, model-driven data management for experimental biology,
Nat. Methods 9 (2012) 245–253.
[3] M. Linkert, et al., Metadata matters: access to image data in the real world, J. Cell Biol.
189 (2010) 777–782.
[4] J. R. Swedlow, et al., Informatics and quantitative analysis in biological imaging, Science
300 (2003) 100–102.
[5] M. D. Wilkinson, et al., The FAIR guiding principles for scientific data management and
stewardship, Sci Data 3 (2016) 160018.
[6] S. Soiland-Reyes, et al., Packaging research artefacts with RO-Crate, Data Sci. 5 (2022)
97–138.
[7] da Silva Santos, et al., FAIR data point: A FAIR-oriented approach for metadata publication,
Data Intell. 5 (2023) 163–183.
[8] S.-A. Sansone, et al., Toward interoperable bioscience data, Nat. Genet. 44 (2012) 121–126.
[9] D. community, nfdi4plants/arc-specification: 1.2, 2023. URL: https://doi.org/10.5281/zenodo.
10091038. doi:10.5281/zenodo.10091038 .
[10] R. Hosseini, et al., FAIR high content screening in bioimaging, Sci Data 10 (2023) 462.
[11] U. Sarkans, et al., Rembi: Recommended metadata for biological images—enabling reuse
of microscopy data in biology, Nature Methods 18 (2021) 1418–1422. URL: http://dx.doi.
org/10.1038/s41592-021-01166-8. doi:10.1038/s41592- 021- 01166- 8 .
[12] P. A. Harris, et al., The REDCap consortium: Building an international community of
software platform partners, J. Biomed. Inform. 95 (2019) 103208.
[13] J. Moore, German-bioimaging/omero-rdf: v0.1.5, 2023. URL: https://doi.org/10.5281/zenodo.
10359688. doi:10.5281/zenodo.10359688 .