IOM–Nano–EHS data templates

A separate set of Excel templates have been developed over the last decade at the Institute of Occupational Medicine IOM and used to gather data in several EU FP7 projects (NANOMMUNE, NanoTEST, ENPRA, MARINA, NanoSolutions, SUN). They are being further adapted for use in more recent H2020 projects (currently PATROLS, GRACIOUS, BIORIMA, RiskGONE and NanoInformaTIX).

These templates (referred to as IOM–Nano–EHS data templates) were originally derived in alignment with earlier (from 2009) JRC–IHCP NanoHub database requirements (built upon the IUCLID model, initially 5.1). These templates were based on the original OECD HT, for a variety of bio assays, and tailored to provide simplified subsets of the complete HT, and provided to the experimentalists for data collection spreadsheet format. This delivers a user friendly and suitably flexible approach whereby end-users entering data could modify the templates for the particular needs of their experimental regimes where necessary, and in liaison with the project’s database administrator. They have successfully provided a practical format for users collecting the results of a variety of physicochemical, in-vitro, in-vivo and eco-toxicology assays for nanoEHS safety assessment. Their flexibility and user friendliness increase user acceptability and utility, but potentially require an additional effort later in the data curation process, due to the need to process more variations in file layout and format to enable upload to the database. Whilst being laid out physically very differently from ISA–Tab, in order to facilitate the collection of data in patterns better reflecting the experimental conditions and data outputs, the templates still inherently share the logical principles and essential metadata features of ISA–Tab, including information on the test method and relevant SOPs as mandatory requirements. To date, the IOM templates have generally collected results for one substance and one assay type in a single Excel spreadsheet file composed of several related worksheets. The first worksheet (“Test conditions”) is organised in the following groups:

1. Experimental test and end point details. These collect general information about the project, work package, test facility, scientist(s) conducting the tests, start and end dates, details of assay name, specific endpoint(s), outcome metric(s), and experimental protocol;
2. Test substance/NM. The name, CASRN, project ID of the substance, with a separate field for additional general material IDs (e.g., JRC representative materials) and the highest concentration used;
3. Information on replicates and controls; Timeline and dosage/treatment concentration. The latter span several cells, as many as required to cover the time points and concentrations used. The names (T1, T2, T3, etc., C1, C2, C3 etc.) are used in data sheets to report the experiment outcomes;
4. Other experimental parameters may be required by the assay being recorded, including key items from the experimental protocol.

There are then experimental results data worksheets. These may differ in detail for different experiments. Generally, the raw data represents the experimental plate layout, indexed by T* and C*, and includes all replicates. The “Test results” worksheet typically includes formulae aggregating measurements’ results across replicates, and is organised in “blocks” (see Section 2.4 for details). The “Test summary” sheet is used to represent derived metrics over several concentrations, e.g., IC50.

Kochev, Nikolay, Nina Jeliazkova, Vesselina Paskaleva, Gergana Tancheva, Luchesar Iliev, Peter Ritchie, and Vedrin Jeliazkov. 2020. “Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the ENanoMapper Database.” Nanomaterials 10 (10): 1908. https://doi.org/10.3390/nano10101908.