Toxicology services

Name Description ELIXIR Node

Cellular and molecular biology are fundamental to ELIXIR's mission. As part of our 2024–28 Programme, we are committed to advancing data services and software for research on nucleic acids, proteins and other biomolecules. This initiative will address new demands for multi-omics and multi-modal analyses, including imaging, by developing methods and partnerships. We will also expand expertise in reusable data and software to incorporate FAIR models, ensuring robust solutions for modelling at all scales. 

The following projects are key to connecting the latest developments with established data resources, unlocking the potential of cellular and molecular biology:

 ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Netherlands
ELIXIR Germany, ELIXIR UK

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. 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 organize a series of online webinars and onsite workshops in collaboration with the ELIXIR Platforms to:

  • demonstrate and disseminate FAIR-ification of toxicological research output (not limited to data);
  • development of guidance for Research Output Management Plans (software, standards, etc) ;
  • develop a roadmap, training, and best practices for making toxicology services ready for EOSC; 
  • optimize and synchronize the toxicology educational resources in an ELIXIR TeSS-based collection; 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.                                    

Therefore, this Implementation Study can be best seen as one continuous BioHackathon. Besides participation in the BioHackathon Europe itself (in which the Toxicology Community has participated already three times), we will specifically organize workshops, working together with toxicologists and ELIXIR experts from Platforms.

 ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR France, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR UK

The ELIXIR Metabolomics Community relies on standards, formats and data treatment solutions development and adoption, but it remains challenging to ensure high-quality reported metadata, sufficiently contextualised results, interoperable and reusable datasets and to integrate these metabolomics data with other omics or studies. 

This project is designed to address these issues and aims to connect key international standards with ELIXIR resources, as well as creating associated community guidelines and training materials. 

Based on the FAIRification framework, activities in the project will:

  • Increase interoperability and reuse of public metabolomics datasets and workflows through enhanced and extended open data standards, resources and new semantic annotations
  • Define, ensure and establish quality control for study baselines in Metabolomics and Exposomics
  • Facilitate metabolomic data interpretation and meta-analysis integration with multi-omics and systems biology studies

As a first necessary step, the project will create a Semantic Metabolomics Data Model to standardise metadata, ensuring unambiguous reuse of metabolomics projects. This model will focus on integrating key ontologies, providing open training initiative and enhancing the interoperability of metabolomics data through the production of open guidelines for annotation steps. By linking with ELIXIR’s Deposition databases, ISA Framework and other services, the project seeks to boost interconnection with ELIXIR platforms, other ELIXIR communities (Systems Biology, Food and Nutrition, Galaxy, Proteomics, Toxicology, Research Data Alliance Focus Group, etc.), the FAIR Cookbook and BioSchemas.org communities. Project outcomes are expected to promote  the emergence of ambitious and innovative semantic-based solutions for inter-comparison of studies in healthcare, clinical and plant domains.

 ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Italy, ELIXIR Spain, ELIXIR France, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR UK, EMBL-EBI