INTOXICOM-WS-2

ELIXIR Toxicology Community

Implementation study-1: Integrating the Toxicology Community into ELIXIR

Grant ID: NL-2023-INTOXICOM

ELIXIR recognized the importance of toxicology and an ELIXIR Toxicology Community has now been established. The Community aims to align FAIR and open data solutions from toxicology with ELIXIR services and resources. To establish this, existing open solutions for data integration across toxicological domains will be disseminated.

This Implementation Study can be best seen as one continuous BioHackathon. Besides participation in the BioHackathon Europe itself the workpackage leaders specifically organise workshops, working together with toxicologists and ELIXIR experts from ELIXIR Platforms.

Abstract / Purpose

New approaches, such as high throughput cell-based assays, omics data and imaging have led to an increase in toxicological data. To innovate risk assessment, exchange and reuse of data between researchers, regulatory and industrial stakeholders becomes increasingly important. To this end, the concept of FAIR data (Findable, Accessible, Interoperable, Reusable) is useful and needed, in particular as biological and chemical data interoperability issues exist. Developing an ELIXIR Community will help to promote access to bioinformatics expertise to accommodate these needs.

ELIXIR recognized the importance of toxicology and an ELIXIR Toxicology Community has now been established [1]. The Community aims to align FAIR and open data solutions from toxicology with ELIXIR services and resources. To establish this, existing open solutions for data integration across toxicological domains will be disseminated.

Additionally, the Community stimulates cross-project collaborations, making platforms, research output, resources, solutions, such as those used for systems toxicology, and data FAIR. Finally, the community fosters the development of missing open community standards, needed to increase the overall FAIRness of data.

A start has been made to interact with ELIXIR resources including FAIRsharing, bio.tools and Bioschemas. Ultimately, the ELIXIR Toxicology Community's ambition is to advance data-rich toxicological research to help address the challenges posed by the risk assessment of chemicals and advanced materials. The Community will provide a platform for researchers and regulators, to collaborate and share data, methods, solutions, standards, and expertise.

This project aims to continue, extend, and scale up the earlier initiated collaborations between ELIXIR activities (Bioschemas.org, bio.tools, TeSS, Systems Biology, ISA tools etc) and the toxicology community. Particularly, we have the following objectives: to organise a series of online webinars and onsite workshops in collaboration with the ELIXIR Platforms to:

demonstrate and disseminate FAIRification of toxicological research output (not limited to data) (WP1);
development of guidance for Research Output Management Plans (software, standards, etc) (WP2);
develop a roadmap, training, and best practices for making toxicology services ready for EOSC (WP3);
optimise and synchronise the toxicology educational resources in an ELIXIR TeSS-based collection (WP4); and
leverage/train the toxicological community on the systems biology resources/tools within ELIXIR to foster (quantitative) adverse outcome pathway design and use of these towards risk assessment (WP5)

Workshop Design

Workshops will be organised following the lessons from the Bring Your Own Data meetings held since 2014 in light of FAIR-ification. While organised independently, the workshops will be held roughly at a 1-2 month interval. To take benefit from other activities, no workshops will be held in the month of the ELIXIR BioHackathon and excluding the summer period, starting from the All-Hands meeting.

Each individual workshop will have the following structure, based on the BYOD approach. Each workshop is preceded by a webinar as a preparatory session 3-4 weeks prior to the workshop, for participants to meet and prepare for the workshop itself. The workshops will be on-site (n=5) for 1-2 full days or from lunch-to-lunch. Each workshop will also involve invited experts from one of the ELIXIR Platforms or other ELIXIR Community to contribute and manage the workshop content.

Afterwards, each workshop will result in a joint effort by the Community members toward a BioHackRXiv report publication (following the defined format), after which can be decided whether to submit to a scientific journal as a final publication (e.g. Toxicological Sciences or ALTEX).

Find here more information about the ELIXIR Toxicology Community.

Duration of this project: 1 January 2024 to 31 December 2024

Elixir nodes involved in this project:

Platform/Community:

Toxicology

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