Abstract
Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.
Key points
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The wizard facilitates the capture of experimental metadata and data via community-agreed templates, ensuring that data types generated by different instruments are linked (spectrometers, flow cytometers, microscopes/plate readers, etc.). SOPs and experimental workflows are also hyperlinked to the templates, supporting data harmonization and interoperability.
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The Template Wizard was evolved with insight and experience gathered over a decade of EU FP7 and H2020 projects addressing nanoscale materials safety.
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Data availability
All material characterization and safety data gathered through the community developed templates during multiple projects are available at the community-recognized repository NanoSafety Data Interface at https://search.data.enanomapper.net/. The following list shows datasets with public licenses and their Zenodo URLs: FP7 NANoREG data (https://search.data.enanomapper.net/projects/nanoreg/; https://zenodo.org/record/3467016), H2020 NanoReg2 data (https://search.data.enanomapper.net/projects/nanoreg2/; https://zenodo.org/record/4713745), H2020 caLIBRAte data (https://search.data.enanomapper.net/projects/calibrate/; https://zenodo.org/record/7193516), H2020 GRACIOUS data (https://search.data.enanomapper.net/projects/gracious/; https://zenodo.org/record/7777590) and H2020 RiskGONE (embargoed until 1 September 2024) (https://search.data.enanomapper.net/projects/riskgone; https://zenodo.org/deposit/8269168). The Zenodo archives are SQL dumps of eNanoMapper database, which could be launched at user machines using the AMBIT docker quick start instructions at https://github.com/ideaconsult/ambit-docker.
Code availability
Open-source packages used in implementation of Nanosafety Data Interface, including the template wizard, are listed below. these are not needed for end-users, who only need a web browser to access the template wizard at NanoSafety Data Interface. Open source NMDataParser (https://github.com/enanomapper/nmdataparser). NMDataParser is a Java library, implementing a configurable parser allowing to convert spreadsheet templates into the internal AMBIT data model, using a JSON file for mapping the objects. The data model can be used for importing into databases, or serialized in different format (W3C RDF, JSON, HDF5). Open source AMBIT software (https://ambit.sourceforge.net/). AMBIT provides chemoinformatics functionality and chemical substance data management (including chemical structures, NMs, unknown or variable composition, complex reaction products or of biological materials and multicomponent chemical substances), all available via REST web services. The eNanoMapper database is compilation of AMBIT software with a specific profile. The REST API also includes the eNanoMapper FAIRification workflow which is used by the template validator. AMBIT/eNanoMapper database Docker distribution (https://github.com/ideaconsult/ambit-docker). Open source Javascript library (https://github.com/ideaconsult/jToxKit) is a client and user interface for the eNanoMapper/AMBIT REST API. Open source (https://github.com/ideaconsult/xlsx-datafill) Javascript library provides template-based data population for Excel XLSX spreadsheets.
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Acknowledgements
Supported by H2020 projects RiskGONE (no. 814425), HARMLESS (no. 953183), Gov4Nano (no. 814401), SABYDOMA (862296), SBD4NANO (862195), PLASTICFATE (no. 965367), POLYRISK (964766), NANOREG2 (no. 646221), PROPLANET (no. 101091842), NanoSolveIT (no. 814572), CompSafeNano (no. 101008099), TWINALT (no. 952404), VISION (no. 857381), KAPPA project EYFORTX2 (no. T001000099-PZ-2021), TEPCAN project (NCBR no. NOR/POLNOR/TEPCAN/0057/ 2019-00), hCOMET project (COST Action, CA 15132), Slovenian Research Agency projects P1-0207 and P1-0184, and by the Norwegian Research Council project NanoBioReal (no. 288768).
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N.J., N.K., L.I. and V.J. contributed to manuscript conceptualization and draft, nmdataparser software development, template wizard development, template cocreation, and eNanoMapper database creation and management. E.L., N.E.Y., E.R.-P. and M.D. contributed to design templates for cytotoxicity (AB, CFE), genotoxicity (CA, HPRT mutation) and endotoxin determination; paper conceptualization and structure, contribution to the manuscript draft, editing and proofreading. E.M. and T.S. contributed to the adaptation of data collection templates for physicochemical data collection and to the section dedicated to the description of physicochemical information. I.V.V. contributed to template building and data interpretation for physicochemical characterization of NMs and CFE assay, and to the manuscript draft and its proofreading. M.J.B. and S.H.D. contributed the HPRT (Swansea layout) and micronucleus template designs, data interpretation for HPRT and micronucleus assays, and proofreading the draft manuscript. M.R.C. and I.R.-M. contributed to the design of the templates and data interpretation for the bioimpedance assay, and to the manuscript draft. E.C. contributed to the design of the templates and data interpretation for the bioimpedance assay, and to the manuscript draft. C.L.B. and C.B. contributed to the design of the template and data interpretation for the in vitro comet assay, to the anticipated results for template reuse section, and to the manuscript draft. R.T. and M.D.A. contributed to the design of the template and data interpretation of micronucleus assay. M.D.A. prepared the “Instruction for use of templates” and contributed to the manuscript draft, editing and proofreading. D.D. contributed to conceptualization, protocol elaboration, literature review and writing sections of the manuscript. S.N. contributed to literature review and writing sections of the manuscript. N.R. contributed to protocol elaboration. A.A. contributed to integrating Ambit with the NSDRA framework for completeness and reusability assessment, wrote the relevant parts to the integration in the manuscript and created Zenodo records for two templates (FRAS and dynamic dissolution). E.W. contributed to manuscript draft editing and proofreading. P.N. contributed to template design and development for omics metadata and manuscript review and editing. V.D.B. contributed to template building and manuscript draft for dynamic dissolution and FRAS assays. A.S. and T.P. contributed to data quality and analysis and to the manuscript draft. K.R. and I.L. contributed to template building for Daphnia culturing, acute and chronic assays, drafted the section on Daphnia templates and contributed to overall manuscript drafting and revision. M.B. contributed to template building for Gov4Nano templates. C.D., A.S.J. and A.S.F. contributed to data review, analyses, templates building and manuscript draft for ‘ORE template’ and ‘ECR template’. N.M. contributed to data review, analyses, templates building and manuscript draft for acute, chronic and bioaccumulation tests on aquatic organisms. M.L.F.-C. contributed to data review, analyses, templates building and manuscript draft for acute and bioaccumulation tests on aquatic organisms. S.R. contributed to template design and input into the manuscript draft.
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Jeliazkova, N. et al. Nat. Nanotechnol. 16, 644–654 (2021): https://doi.org/10.1038/s41565-021-00911-6
Kochev, N. et al. Nanomaterials 10, 1908 (2020): https://doi.org/10.3390/nano10101908
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Collins, A. et al. Nat. Protoc. 18, 929–989 (2023): https://doi.org/10.1038/s41596-022-00754-y
Longhin, E. M. et al. Front. Toxicol. 4, 981701 (2022): https://doi.org/10.3389/ftox.2022.981701
Ostermann, M. et al. Sci. Rep. 10, 142 (2020): https://doi.org/10.1038/s41598-019-56705-3
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Supplementary Methods, Figs. 1–10 and instructions for the use of templates available in the Nanosafety Data Interface.
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Data entry templates.
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Jeliazkova, N., Longhin, E., El Yamani, N. et al. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials. Nat Protoc 19, 2642–2684 (2024). https://doi.org/10.1038/s41596-024-00993-1
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DOI: https://doi.org/10.1038/s41596-024-00993-1
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