FAIRification of multi-omics metadata

Workshop details
  • Date: Monday, September 12th
  • Time: 17:00 to 20:00 CEST
  • Format: Virtual
  • Gary Saunders, EATRIS-ERIC Data Director (The Netherlands)
  • Emanuela Oldoni, EATRIS-ERIC Scientific Programme Manager (The Netherlands)
  • Anna Niehues, Bioinformatician at Radboud University Medical Center (The Netherlands)
  • Metadata FAIRification from the perspective of multi-omics data owners and researchers
  • The other omics / multi-omics
  • Relevance of the data and software management
  • Training

An increasing number of studies employ multi-omics profiling approaches. Multi-omics data sets can serve as invaluable resources for research, if shared in a findable, accessible, interoperable, and reusable (FAIR) manner.

FAIR sharing of omics data is facilitated by archives such as EMBL-EBI’s PRoteomics IDEntifications database (PRIDE), MetaboLights and the European Genome-phenome Archive (EGA), and by data and metadata standards developed by different standardisation initiatives. Bioinformatics tools such as the Investigation/Study/Assay (ISA) metadata framework allow creation of metadata that are compatible with these standards.

An EATRIS-ERIC flagship project, EATRIS-Plus is aiming to advance the field of personalised medicine by addressing bottlenecks in multi-omics research including data stewardship and adoption of FAIR principles. EATRIS-Plus’ multi-omics demonstrator cohort comprises various -omics technologies. The FAIRification of the associated experimental metadata will serve as a use case in this workshop.

Challenges for researchers seeking to create FAIR multi-omics metadata include finding (open) metadata standards and suitable controlled vocabularies for various kinds of -omics data and bringing together many of these standards when describing multi-omics data sets. Applying existing tools for metadata creation can be challenging for researchers with limited bioinformatics or programming experience. Additionally, the multi-omics field is developing rapidly calling for continuous dialogue between researchers, clinicians, data and archive managers, and tool developers.

During this workshop, we will review these challenges as well as solutions based on multi-omics use cases and bring data owners together with data managers and tool developers. Invited speakers will present an overview of the landscape of resources that help researchers create FAIR multi-omics metadata. We will then follow up by identifying gaps in the field from a researcher’s perspective and discuss strategies to close these gaps.

Expected outcomes:

  • Identification of the common challenges and themes when addressing multi-omics metadata FAIRification
  • With a focus on the EATRIS-Plus use case, finding real-world examples of where FAIRification metadata challenges are present and developing strategies to tackle these
  • Increase awareness of available tools and solutions to increase the FAIRification of multi-omics metadata tools, solutions, and frameworks
  • We will write a brief summary of this workshop to summarize scenarios, take-homes, and next steps in the drive towards FAIR metadata for multi-omics datasets, possibly  by creating new content in the form of recipes for the Elixir FAIR cookbook
Target Audience
  • Bioinformaticians
  • Project coordinators
  • Bioinformatics service owners
  • Biomedical researchers
  • Data providers
Invited speakers

Allyson Lister, FAIRsharing Coordinator – Content & Community, Oxford e-Research Centre, University of Oxford, Data Readiness Group

Anna Niehues, Bioinformatician at Radboud university medical center

Claire O’Donovan, Metabolomics Team Leader, EMBL-EBI

Deepti J. Kundu, Scientific curator Proteomics resources, EMBL-EBI

Jildau Bouwman, Senior scientist systems biology, TNO

Joeri van der Velde, Postdoc bioinformatician at the University Medical Center Groningen, (The Netherlands)

Juan Antonio Vizcaino, Proteomics Team Leader, EMBL-EBI

Philippe Rocca-Serra, Group Co-Investigator, Oxford e-Research Centre, Associate Member of Faculty, Department of Engineering, University of Oxford (United Kingdom)

Veronika Suni, Bioinformatician at the Machine Learning in Biomedicine group, University of Helsinki (Finland)

17:00Welcome, overview of program, introduction of speakers
17:10The multi-omics data FAIRification process – two use cases from the bioinformatics researcher’s perspective

FAIRification of the EATRIS-Plus multi-omics demonstrator cohort
Anna Niehues
The iCAN Digital Precision Cancer Medicine project
Veronika Suni
17:40Tools, services, and resources to facilitate multi-omics data FAIRification

FAIRsharing: discover and curate an ecosystem of research standards and databases
Allyson Lister
10 years of ISA: Lessons learned from the community and recent developments
Philippe Rocca-Serra
18:10FAIRification practices at omics data repositories

MetaboLights and FAIRification
Claire O’Donovan
The PRIDE database: Enabling FAIR practices for proteomics data
Deepti J. Kundu and Juan Antonio Vizcaino
18:50Interactive tools to capture and share metadata of multi-omics studies using templates

Sharing study meta-data for biologists: the Phenotype database as solution

Jildau Bouwman
FAIR Genomes and MOLGENIS as a FAIRification platform
Joeri van der Velde
19:20Interactive panel discussion: Connect the tooling landscape, identify gaps, and define next steps in the drive towards FAIR metadata for multi-omics datasets
All speakers
20:00End of workshop