University of Massachusetts Medical School Faculty Publications
UMMS Affiliation
Program in Molecular Medicine
Publication Date
2021-07-28
Document Type
Article Preprint
Disciplines
Biochemistry, Biophysics, and Structural Biology | Bioimaging and Biomedical Optics | Biotechnology | Cataloging and Metadata | Data Science | Laboratory and Basic Science Research | Research Methods in Life Sciences
Abstract
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.
Keywords
metadata, research data management, FAIR principles, microscopy
Rights and Permissions
Distributed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license.
Source
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
Journal/Book/Conference Title
arXiv
Repository Citation
Kunis S, Hansch S, Schmidt C, Wong F, Strambio-De-Castillia C, Weidtkamp-Peters S. (2021). MDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools [preprint]. University of Massachusetts Medical School Faculty Publications. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/2091
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 4.0 License.
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioimaging and Biomedical Optics Commons, Biotechnology Commons, Cataloging and Metadata Commons, Data Science Commons, Laboratory and Basic Science Research Commons, Research Methods in Life Sciences Commons
Comments
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.