Enalos Cloud Platform Transnational Access Services Through NanoCommons H2020 Infrastructure Project

NanoCommons is a research e-infrastructure project offering access to high quality nanoinformatics tools and services for nanotechnology and nanosafety stakeholders (academia, industry, regulators). It is user-led, offering and developing the services needed by the user community of nanotechnology, nanosafety and related fields. NanoCommons is built on 3 main pillars: joint research activities, networking activities and transnational access services, covering four categories relevant for nanosafety assessment:
• experimental workflows design and implementation;
• data processing and analysis;
• data visualisation and predictive toxicity;
• data storage and online accessibility.
These services are designed to promote data FAIRness (Findable, Accessible, Interoperable, and Reusable), a key NanoCommons goal, that can be made Open through the NanoCommons Knowledgebase. Thus, NanoCommons provides innovative solutions for data mining, harmonisation, utilisation and re-utilisation, including incorporation of a range of modelling and decision support tools that require and/or can produce organised, high-quality datasets. A number of online training tools have been developed for each of the offered services to help users chose and use the services relevant to their needs. The NanoCommons help-desk and training library shall bridge academic research with industry and regulators, as recommended by the EU NanoSafety Cluster‘s “Closer to the Market” Research Roadmap serving the Safe-by-Design concept in nanotechnology.

The aim is to introduce unique approach of the ACEnano Knowledge Protocols and Data
warehouse designed to disseminate protocols and their variations and to store, manage and
share data for physico-chemical characterisation of nanomaterials under standard conditions
as well as at different life stages.

NanoCommons (Horizon 2020 INFRAIA, project no. 731032) aims to provide a standardised, reproducible and interoperable way to access available data, knowledge, analysis and modelling tools that have been adapted and verified as suitable for application to nanomaterials.
One of the major goals is to reduce the fragmentation of nanosafety related data and knowledge by aligning and semantically linking available resources major European and international nanosafety projects and infrastructures, providing new harmonized resources when needed and ensuring access following the FAIR principles (Findable, Accessible, Interoperable and Re-usable) whenever possible in an open and free manner. Outputs to be shared via the NanoCommons knowledge infrastructure include: i) Central data access to stored data or linked data sources via a variety of mechanisms (e.g. web interfaces, application programming interfaces), ii) Metadata-rich datasets from experiments and modelling/simulations, iii) Protocols and Standard Operating Procedures, iv) Quality Assurance, v) Concepts, guidance and templates for data curation, vi) Automated annotation pipelines, and vii) Data standards. This integrated design offers easy and harmonized access to a variety of datasets (physicochemical, hazard, exposure, fate) as well as data management, data mining and data visualisation tools to researchers from academia and industry, as well as regulators, ensuring their optimal use and joint development.

ACEnano knowledge infrastructure (KI) supports the activities related to data collection and method optimisation in the area of physicochemical characterisation of nanomaterials. The KI provides a central place to access harmonised and standardised methods and data, supporting the implementation of Findable, Accessible, Interoperable and Reusable (FAIR) data principles, the reproducibility and documentation process towards the goal of generating reference resources for nanomaterials risk assessment.
The KI includes instances to accommodate data and protocols. The protocols database facilitates adding, sharing and comparing methods in a questionnaire-like format guiding users through the documentation process from starting material identification to sample preparation, measurement and data processing. The data warehouse offers long-term storage of the results in a reusable format that are directly linked to the methods applied.
A public version of the data warehouse is being integrated in the NanoCommons ecosystem. By semantic annotation and linking, this guarantees harmonisation and interoperability with other data sources of the EU NanoSafety Cluster like the eNanoMapper and NanoFASE.
The development of the KI is supported by ACEnano (EU Horizon 2020 NMBP project no. 720952), while its availability to a wider community is assured by the activities in NanoCommons (Horizon 2020 INFRAIA project no. 731032).

This UoB Transnational Access service is focussed on services related to dataset management and accessibilty - including the use of electronic laboratory notebooks, the annotation of existing datasets with ontology terms to facilitate the dataset integration into the NanoCommons database, support in the analysis of datasets from a statistical viewpoint, and support in making data FAIR - Findable, Accessible, Interoperable and Re-usable. Our data management services span the entire data lifecycle - from exprimental design through data generation, analayis and storage, linking to experimental protocols and biobliographnic metadata, and long-term deposition of datasets. Services can be acccessed individually or as a packaged tailored to individual needs. Services are applicable to indivudal datasets or to entire portolios of data arising from research projects or teams.

NanoCommons – Assistance with Data Management & Nanoinformatics Tools

Bringing nano-enabled developments to the market still faces challenges along up-scaling processes and safety evaluation [1] and needs to be addressed in a structured way [2]. In addition, a major aim is to assess the safety profiles of engineered nanomaterials (ENMs) at low, nonlethal dosages and extended repetitive exposures, which could help to understand long-term consequences of ENMs’ interactions with biological environments and further expedite their translation into products and applications.
To enable this translation, data plays a prominent role. And here is where NanoCommons[3], the e-infrastructure project, as one of the three EU-H2020 data relevant projects (together with NanoSolveIT and NanoinformaTIX) can help nanosafety researchers from industry, academia and regulatory bodies to access the state-of-the-art data management expertise. Thus, users/collaborators can take advantage of the NanoCommons services, facilities and knowledge to advance their work, solve problems and take their research to the next level.
Within this contribution, it is presented, how NanoCommons, by means of its transnational actions (TAs), brings benefits to its users/collaborators: (i) EU funded access to expertise in data management and nanoinformatics tools; (ii) Facilitate open access data to help reduce duplication of tests, regulation, animal-testing, bureaucracy…; (iii) Assistance with capture and databasing of data to comply with EU open data initiatives and achieve FAIR data principles[4]; (iv) model development; and many more.

[1] Falk, A., Schimpel, C., Haase, A., Hazebrouck, B., Fito López, C., Prina-Mello, A., Savolainen, K., Sips, A., Lopez de Ipiña, J., Lynch, I., Charitidis, C., Visser, G. (2016). “Closer to the market”-Roadmap (CTTM). Zenodo. DOI: https://zenodo.org/record/1493492
[2] Schimpel, C., Resch, S., Flament, G., Carlander, D., Vaquero, C., Bustero, I., Falk, A. (2018). A methodology on how to create a real-life relevant risk profile for a given nanomaterial. Journal of Chemical Health and Safety, 25(1), 12-23.
[3] NanoCommons: https://www.nanocommons.eu/
[4] https://www.openaire.eu/how-to-make-your-data-fair

Jaqpot is a computational platform developed by NTUA, that facilitates in silico modelling, by enabling the systematic production, collection, organization, validation, storage and sharing of predictive models, with emphasis on predictive toxicology. A particular type of models that can be hosted in the Jaqpot environment are the so called Physiologically-based pharmacokinetic (PBPK) models which are used for describing and predicting the biokinetics of chemicals and pharmaceutical drugs. PBPK modelling of Nanomaterials (NMs) is more challenging due to their complicated in vivo disposition properties compared to conventional chemicals. The scientific community has addressed this problem, mainly by augmenting the system of differential equations for describing the concentration of NPs in different tissues and organs as a function of time. One such PBPK model has been developed by Li et al. (2014) for modelling the biokinetics of polyethylene glycol-coated polyacrylamide (PAA-peg) NPs in the rat. In this work we present the implementation of this PBPK model as a web service in the Jaqpot modelling platform. This development is part of the transnational access (TA) activities of the NanoCommons EU Horizon 2020 project, aiming to increase the visibility of the model and allow simulation and testing of different biodistribution scenarios by users.

Here we present the three services that CEH offers through NanoCommons transnational access that include (i) Ecotoxicological Laboratory Workflows, (ii) Data processing & analysis (EcoToxicology), and (iii) Predictive Eco-NanoToxicology.