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dc.contributor.authorKunis, Susanne
dc.contributor.authorHansch, Sebastian
dc.contributor.authorSchmidt, Christian
dc.contributor.authorWong, Frances
dc.contributor.authorStrambio-De-Castillia, Caterina
dc.contributor.authorWeidtkamp-Peters, Stefanie
dc.date2022-08-11T08:08:28.000
dc.date.accessioned2022-08-23T15:56:02Z
dc.date.available2022-08-23T15:56:02Z
dc.date.issued2021-07-28
dc.date.submitted2021-11-10
dc.identifier.citation<p>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. <a href="https://arxiv.org/abs/2103.02942" target="_blank" title="view preprint on arXiv">View preprint on arXiv</a></p>
dc.identifier.doi10.48550/arXiv.2103.02942
dc.identifier.urihttp://hdl.handle.net/20.500.14038/29885
dc.description<p>This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.</p> <p>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.</p>
dc.description.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.
dc.language.isoen_US
dc.rightsDistributed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/
dc.subjectmetadata
dc.subjectresearch data management
dc.subjectFAIR principles
dc.subjectmicroscopy
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioimaging and Biomedical Optics
dc.subjectBiotechnology
dc.subjectCataloging and Metadata
dc.subjectData Science
dc.subjectLaboratory and Basic Science Research
dc.subjectResearch Methods in Life Sciences
dc.titleMDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools [preprint]
dc.typePreprint
dc.source.journaltitlearXiv
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=3109&amp;context=faculty_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/faculty_pubs/2091
dc.identifier.contextkey25856017
refterms.dateFOA2022-08-23T15:56:03Z
html.description.abstract<p>While 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.</p>
dc.identifier.submissionpathfaculty_pubs/2091
dc.contributor.departmentProgram in Molecular Medicine


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Distributed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license.
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