LISTER: Semi-automatic metadata extraction from annotated experiment documentation in eLabFTW

Prof. Dr. Holger Gohlke

(Heinrich-Heine-Universität Düsseldorf, Institut für Pharmazeutische und Medizinische Chemie)

Documenting experiments with metadata for a sustainable RDM practice requires user involvement. One of the main hurdles for the user is to annotate metadata from scratch manually. In our approach, we attempt to minimize this user involvement. We utilize the electronic lab notebook eLabFTW to create an RDM workflow along with an annotation mechanism for metadata extraction. The workflow includes the use of annotated SOP and Materials and Methods (MM) sections as templates  that can be reused and/or readapted for comprehensive and efficient experiment descriptions. We organize these descriptions according to an ISA-based framework (System, Project, Study, and Publication). Metadata can then be extracted automatically from the experiment descriptions based on the annotations, using the app LISTER we developed. We demonstrate RDM workflow showcases for the research fields of molecular simulations and wetlab biochemistry. Later, the corresponding experiment research data are uploaded with its rich-metadata context into a research data portal, allowing research data to be findable and accessible with minimized efforts from the user’s end.