MDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools

TL;DR

This paper introduces MDEmic, a flexible metadata editing tool integrated into OMERO, to enhance FAIR compliance in microscopy data management through improved metadata annotation and standardization.

Contribution

The paper presents MDEmic, a new tool for microscopy metadata editing that supports flexible, standardized metadata annotation, integrated into OMERO for practical FAIR data management.

Findings

MDEmic is integrated into OMERO as OMERO.mde.

MDEmic supports flexible metadata adjustment for microscopy data.

Use case demonstrates improved metadata management in a Membrane Dye Database.

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.