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

Periodic Reporting for period 1 - NanoCommons (The European Nanotechnology Community Informatics Platform: Bridging data and disciplinary gaps for industry and regulators (NanoCommons))

Reporting period: 2018-01-01 to 2019-06-30

Nanotechnologies represent major areas of investment and growth for the European economy. Recent advances have enabled confidence in the understanding of what constitutes toxicity of engineered nanomaterials (ENMs) in relation to health and environmental hazards. However, nanotechnology and nanosafety communities remain disparate and unconnected, whilst knowledge and data remain fragmented and inaccessible. The field, and indeed the European open knowledge economy, requires conversion of these scientific discoveries into legislative frameworks and industrial applications, which can only be achieved through concerted efforts to integrate, consolidate, annotate and facilitate access to, and re-use of, the currently disparate datasets. To address this gap, 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 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; the Networking Activities (NA) ensuring that NanoCommons serves the needs of its users and stakeholders, and the Transnational Access (TA) programme which provides funded access to the tools, models and services and the support needed to run them.
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, spanning from NMs manufacture and characterisation through safety assessment and risk assessment, accessible to experimentalists, modellers, risk assessors, industry and educators (JRA).
(2) To provide funded and expert-supported Access to a range of data / knowledge management tools and nanoinformatics services integrated and developed via the JRA to the widest possible range of stakeholders across industry and SMEs, modellers, experimentalists, regulators and educators, including at the earliest stages of workflow design and including guidance on data quality assurance including data audits and method assessment/evaluation (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 first 18 months of the NanoCommons project focused on getting all partners working on optimisation of their initial services and tools for provision via the TA programme. Integration of these models, tools, and services into the NanoCommons catalogue of services, and communicating with the NanoCommons Knowledge Base that underpins the knowledge management services offered by NanoCommons, was the priority for year 1, to enable the successful launch of the 1st call for funded TA in early 2019.

Significant developmental efforts were invested in developing the knowledge management infrastructure and supporting structures such as the nanosafey and nanoinformatics ontologies, the quality assurance and quality control processes and the workflows for dataset upload and semantic mapping to the NanoCommons Knowledge base. This was underpinned by development of the training materials and training programme to support stakeholders, and the development of a sustainability strategy for the NanoCommons research infrastructure to provide long-term stability for the datasets, models, ontologies and related nanoinformatics ecosystem.

The NanoCommons knowledge base has been developed and the first version has been implemented using the BioXM Knowledge Management Environment. Work is ongoing to link it with other major data sources, access options to make data available via application programming interfaces callable by modelling and risk assessment tools, as well as integration of the NanoCommons TA services catalogue, thereby building the one-stop shop for finding integrated data and software resources. Datasets currently being integrated into NanoCommons include NanoMILE and NanoFASE, eNanoMapper and its implementations for other projects (e.g. NANoREG) and ACEnano.

As a research infrastructure project, a core aspect of our mission is to support the nanosafety research community in improving their data management approaches – thus, NanoCommons has published its Data Management Plan open access, to facilitate other EU-funded and national nanosafety projects to adopt the current best practice. As our DMP evolves we are releasing updates. Several projects have adopted our DMP for their projects, including RiskGONE and Gov4Nano.
Several of our modelling approaches and advances have also been published within the first period of the project, with several more publications in advanced stages of progress. The first paper, on a safe-by-design tool for functionalised ENMs, presents a validated and predictive nanoinformatics model for the accurate prediction of the biological and toxicological profile of decorated multi-walled carbon nanotubes. The nanoinformatics workflow was fully validated according to the OECD principles before it was released online via the Enalos Cloud platform and through NanoCommons TA. The second paper presents a novel read-across methodology for the prediction of toxicity related end-points of ENMs that employs a single criterion or multiple criteria for defining similarities among ENMs, without the need to pre-define a read-across hypothesis. The automated method searches over a space of alternative hypotheses, and determines the one providing the most accurate read-across predictions. Only two parameters are user-defined: the balance between the level of predictive accuracy and the number of predicted samples, and the similarity criteria, which define the neighbours of a target ENM.
NanoCommons has also taken over the updating and onward development of the eNanoMapper ontology. The first major release under the supervision and management of NanoCommons was the 5.0 release, made on 13th September, 2018. This release included the updated CHEMINF ontology and a number of new terms, following needs identified from collaboration projects including NanoFASE and had 12,536 new terms. The second major release (6.0 release) was made on 30th August, 2019. This release again added a number of terms used by other p
NanoCommons has the unique potential to deliver a step-changing impact for the emerging nanoinformatics in nanosafety community. It will remove barriers from nanosafety-related regulatory & industry processes by revolutionising data capture, management & sharing. NanoCommons will achieve this through:
(i) its integration of disparate datasets, tools and modelling approaches from across the 60+ projects related to nanosafety-funded across FP6, FP7 and H2020 (NA),
(ii) its development of an integrated KnowledgeBase to facilitate development and application of regulatory tools such as QSARs, grouping and read-across (JRA); and
(iii) its efforts to support Users (all stakeholders: academia, industry, regulators etc.) in utilisation of the appropriate tools and supporting expertise to address their data and research needs (TA).