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The European Nanotechnology Community Informatics Platform: Bridging data and disciplinary gaps for industry and regulators (NanoCommons)

Periodic Reporting for period 2 - NanoCommons (The European Nanotechnology Community Informatics Platform: Bridging data and disciplinary gaps for industry and regulators (NanoCommons))

Reporting period: 2019-07-01 to 2020-12-31

Nanotechnologies, as part of the advanced materials portfolio, represent major areas of investment and growth for the European economy. The field and the European open knowledge economy requires conversion of the emerging scientific discoveries into legislative frameworks and industrial applications, which can only be achieved through concerted efforts to integrate, annotate and facilitate access and re-use of the currently disparate datasets. NanoCommons brings together academia, industry and regulators to facilitate pooling and harmonising of methods and data for modelling, safe-by-design product development and regulatory approval purposes, thereby driving best practice and ensuring maximum access to data and tools.

NanoCommons (see Figures 1 and 2) is structured into three main pillars of activity, namely the Joint Research Activities (JRA) developing state of the art inter-operable data management and nanoinformatics tools for prediction of nanomaterials’ impacts on humans and the environment; the Networking Activities (NA) ensuring that the NanoCommons research infrastructure continues to evolve and adapt to best serve the needs of its users and stakeholders, and the Transnational Access (TA) programme (see Figure 3) which provides funded access to the tools, models and services to meet stakeholder nanosafety nanoinformatics needs.

NanoCommons’s objectives under JRA, NA and TA are as follows:
(1) To develop an integrated data and methods capture, management and nanoinformatics platform to enhance the accessibility and reusability of nano-related data and associated protocols (JRA).
(2) To provide funded and expert-supported Access to a range of data / knowledge management tools and nanoinformatics services to the widest possible range of stakeholders (TA).
(3) To continuously assess community needs in terms of services required, and align training offers, tools integrated into the TA portfolio and demonstration case studies to address these needs (NA).
The middle 18 months of the NanoCommons project (months 19-36, July 2019 – December 2020) focused on consolidating our activities and pushing forward with our agenda to develop tools and supports for nanosafety researchers across the entire nanosafety data lifecycle (see our data lifecycle and data management services schematic – Figure 4), and raising awareness of the tools and services across the nanosafety, nanomedicine, materials modelling and materials characterisation research communities. This period was quite strongly affected by the Covid-19 pandemic, which meant that all travel and face to face meetings had to be postponed, and all outreach, training and TA activities had to be fully online. However, the NanoCommons team rose to the challenges of the pandemic well, and led a very well-attended training webinar series across 2020 for the nanosafety community in collaboration with the NanoSafety Cluster Working Group A. All training materials are available through the NanoCommons User Handbook [1] and the Elixir TeSS portal [2], and the webinar series will continue throughout 2021.

Building on the excellent work in period 1 to develop NanoCommons Application Programming Interfaces, several further models and tools were developed and integrated using Jaqpot [3] and Enolas [4] platforms for modelling, and graphical user interfaces and Jupetyr notebooks were implemented to support model integration and use by non-expert users across academic, industry and regulators. A further advance has been to develop KNIME nodes for each model, tool and database to allow linkage into user friendly and fully automated workflows. This is shown schematically for the NanoCommons Risk Assessment tool [3] in Figure 5, which integrates the nanomaterials exposure scenarios from the FP7 GUIDEnano project, physiologically based pharmacokinetic (PBPK) models developed within NanoCommons and the NanoPharos database for modelling descriptors and outputs developed jointly by NanoCommons and H2020 nanoinformatics project NanoSolveIT. KNIME is a graphical user interface to create workflows combining different tools without the need for user-provided coding. More NanoCommons KNIME nodes will be developed giving KNIME users access to the sophisticated NanoCommons services without the need to code the API access to the microservices themselves.

Having successfully developed and published [4] the concept of an extension of the IUPAC International Chemical Identifier (InChI) to nanomaterials, also called NInChIs (see Figure 6), NanoCommons coordinator and partners have now been invited by the InChI Trust to establish a formal working group and to develop the NInChI towards a standard for implementation into a subsequent release of the InChI standard. This would be a significant and important outcome for the project, as such standard identifiers could be utilised in many applications including in publishing, modelling, nanomaterials marketplaces etc. The NInChI generator tool [5] is available for testing and feedback, and is being further refined and developed.

Significant efforts were invested in developing the knowledge management infrastructure and supporting structures such as the nanosafety and nanoinformatics ontologies, the processes and the workflows for dataset upload and semantic mapping to the NanoCommons Knowledge base, and the training materials and training programme to support stakeholders, and the sustainability strategy for the NanoCommons research infrastructure. NanoCommons will also continue its extremely successful processes of development of key publications in collaboration with the broader community will continue in the final period, with follow-up papers on the InChI for nanomaterials (NInChI), metadata templates, sustainability of tools and services (e.g. via containerisation) and more planned over the coming months. At least 1 more special issue will also be organised as an effective means to showcase our outputs and activities.

[1] https://www.nanocommons.eu/e-infrastructure/user-guidance-handbook/
[2] https://tess.elixir-europe.org/content_providers/nanocommons
[3] http://enaloscloud.novamechanics.com/nanocommons/exposure/
[4] https://doi.org/10.3390/nano10122493
[5] http://enaloscloud.novamechanics.com/nanocommons/NInChI/
After three years, NanoCommons provides a fully operational infrastructure to its users. Importantly, most of the key work promised at the outset of NanoCommons has now been achieved, and ongoing efforts to further extend and consolidate these offers of services and tools are underway.

NanoCommons has demonstrated its value to the community and its ability to address end-user and stakeholder needs in a cost-effective and streamlined manner within the large number of transnational access (TA) projects finalised or already producing major results in 2020. The added-value of the NanoCommons community infrastructure will continue to arise from further integration of the various tools and services, including those developed by other consortia and projects. Thus, our driving focus in the final 18 months of the project will be delivery of community support services, integration and consolidation of our offer, and working to ensure uptake by the community and sustainability of the tools, services and core infrastructure.
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