Journal Article

Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research

Walker, Lee, Exner, Thomas E, Weltring, Klaus M, Wiesner, Mark R, Reilly, Katie, Amos, Jaleesia D, Friedrichs, Steffi, Johnson, Litty, Günday-Türeli, Nazende, Svendsen, Claus, Brajnik, Maja, Papadiamantis, Anastasios G, Martinez, Diego S T, Punz, Benjamin, Lynch, Iseult, Dokler, Joh, Ogilvie Hendren, Christine, Green Etxabe, Amaia, Himly, Martin

2025

Overview

Nanosafety assessment, which seeks to evaluate the risks from exposure to nanoscale materials, spans materials synthesis and characterisation, exposure science, toxicology, and computational approaches, resulting in complex experimental workflows and diverse data types. Managing the data flows, with a focus on provenance (who generated the data and for what purpose) and quality (how was the data generated, using which protocol with which controls), as part of good research output management, is necessary to maximise the reuse potential and value of the data. Instance maps have been developed and evolved to visualise experimental nanosafety workflows and to bridge the gap between the theoretical principles of FAIR (Findable, Accessible, Interoperable and Re-usable) data and the everyday practice of experimental researchers. Instance maps are most effective when applied at the study design stage to associate the workflow with the nanomaterials, environmental conditions, method descriptions, protocols, biological and computational models to be used, and the data flows arising from study execution. Application of the InstanceMaps tool (described herein) to research workflows of increasing complexity is presented to demonstrate its utility, starting from (i) documentation of a nanomaterial’s synthesis, functionalisation, and characterisation, over (ii) assessment of a nanomaterial’s transformations in complex media, (iii) description of the culturing of ecotoxicity model organisms Daphnia magna and their use in standardised tests for nanomaterials ecotoxicity assessment, and (iv) visualisation of complex workflows in human immunotoxicity assessment using cell lines and primary cellular models, to (v) the use of the instance map approach for the coordination of materials and data flows in complex multipartner collaborative projects and for the demonstration of case studies. Finally, areas for future development of the instance map approach and the tool are highlighted.

• Publisher: Beilstein-Institut zur Föerderung der Chemischen Wissenschaften,Beilstein-Institut
• Subject: data collection and quality control / data provenance / Datasets / Documentation / experimental workflow visualisation / fair / Full Research Paper / Metadata / nanomaterial life cycle stages / Nanomaterials / Nanoscience / Nanotechnology / Researchers / study design / Toxicity