MDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools [preprint]
UMass Chan AffiliationsProgram in Molecular Medicine
research data management
Biochemistry, Biophysics, and Structural Biology
Bioimaging and Biomedical Optics
Cataloging and Metadata
Laboratory and Basic Science Research
Research Methods in Life Sciences
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AbstractWhile the FAIR principles are well accepted in the scientific community, the implementation of appropriate metadata editing and transfer to ensure FAIR research data in practice is significantly lagging behind. On the one hand, it strongly depends on the availability of tools that efficiently support this step in research data management. On the other hand, it depends on the available standards regarding the interpretability of metadata. Here, we introduce a tool, MDEmic, for editing metadata of microscopic imaging data in an easy and comfortable way that provides high flexibility in terms of adjustment of metadata sets. This functionality was in great demand by many researchers applying microscopic techniques. MDEmic has already become a part of the standard installation package of the image database OMERO as OMERO.mde. This database helps to organize and visualize microscopic image data and keep track of their further processing and linkage to other data sets. For this reason, many imaging core facilities provide OMERO to their users. We present a use case scenario for the tailored application of OMERO.mde to imaging data of an institutional OMERO-based Membrane Dye Database, which requires specific experimental metadata. Similar to public image data repositories like the Image Data Resource, IDR, this database facilitates image data storage including rich metadata which enables data mining and re-use, one of the major goals of the FAIR principles.
Kunis S, Hänsch S, Schmidt C, Wong F, Strambio-De-Castillia C, Weidtkamp-Peters S. MDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools. arXiv preprint arXiv:2103.02942. 2021 Mar 4. View preprint on arXiv
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/29885
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.
The PDF available for download is Version 3 of this preprint. The complete version history of this preprint is available at https://arxiv.org/abs/2103.02942.