Integration of an electronic notebook with automated metadata extraction: application of FAIR-by-design principles to O-PTIR spectroscopy at SISSI-Bio laboratory

This thesis presents a model for the integration of an electronic notebook with automated metadata extraction as a practical application of FAIR-bydesign principles to O-PTIR spectroscopy. The project has been developed in the framework of the SISSI-Bio laboratory, the infrared laboratory of Elettra Sicrotrone Trieste. The model presented here was specifically developed for use in a user-oriented facility as the SISSI-Bio laboratory. Chapter 1 introduces the concept of Open Data in scientific research, highlighting its relationship with the principles of FAIR-by-design. These concepts are discussed particularly within the framework of the Horizon Europe guidelines for Open data. Chapter 2 describes the research environment of the SISSI-Bio laboratory at Elettra Sincrotrone, where thanks to a partnership between Area Science Park and Elettra Sincrotrone Trieste, within PRP@CERIC project, a state-of-the-art infrared facility is currently operative and open to external users proposals. Chapter 3 describes the model I developed ad hoc for one of the techniques available at SISSI-Bio, namely O-PTIR spectro-microscopy. The model integrates the python APIs of ElabFTW, a versatile electronic logbook enabling metadata storage and automated extraction with the hdf5 architecture of ptir files. A practical application is presented through real datasets, kindly provided by SISSI-Bio CERIC-ERIC users and taken from in house research. The first dataset used for data fairification consists on O-PTIR experiments on bone tissue sections embedded in a hard polymer matrix. The second dataset to which the fairification model has been applied is related to in-house research experiments done in collaboration with researchers of Trieste University. We analyzed nanostructured superassemblies of heterochiral dipeptides through O-PTIR microscopy. The two datasets here shown represent good examples of SISSI-Bio O-PTIR applications, serving as representative case studies of several experiments in biomedical, cultural heritage and environmental science. The conclusions of this thesis briefly summarize the main achievement and propose new ideas for extending the model to other techniques available at SISSI-Bio and for integrating it to the PRP@CERIC infrastructure