Overview of ELIXIR and of two FAIR-related activities to the NSF FAIR for USA workshop, 17 Feb 2022

1. www.elixir-europe.org
ELIXIR: bringing together life science
resources from across Europe
t
Prof. Susanna Assunta Sansone,
t
ELIXIR Interoperability Platform ExCo;
ELIXIR-UK Node - Management Committee Member
t
Professor of Data Readiness,
Department of Engineering Science, University of Oxford, UK
NSF FAIR for US Workshop, 17 February 2022
Slides:
https://www.slideshare.net/SusannaSansone

2. ELIXIR - a sustainable infrastructure for biological data

3. What services do ELIXIR offer?
Databases and Data Resources
Interoperability Resources
Bioinformatics Tools
Compute Capabilities
Bioinformatics Training Opportunities

4. ELIXIR Nodes: Connecting national data infrastructures
ELIXIR Nodes are the permanent structure in ELIXIR:
• Provide the services accessed by life scientists
• Act as national coordinating entities
• Bring together experts via Platforms,
Communities and Focus Groups
ELIXIR implement Europe-wide activities with
significant value to Nodes

5. ELIXIR Communities connect infrastructure with
life-science research experts
• Formed around domain experts in ELIXIR Nodes
(including non-ELIXIR partners)
• Provide a mechanism for long-term collaborations
with other ESFRIs (European Strategy Forum on
Research Infrastructures) and large-scale initiatives
• Drive service developments in the ELIXIR Platforms
• Provide framework to develop and maintain
community standards
Food & Nutrition
+ Toxicology

6. How is ELIXIR funded
As a distributed infrastructure, ELIXIR has a mixed funding model with contributions
coming from a number of mostly public sources

7. Commissioned Services in the 2019-23 ELIXIR Programme
● 25 projects ongoing with
22 Nodes
● 4,0M EUR
● 21 project completed
● 7 projects ongoing with
20 Nodes
● 2,3M EUR
● 6 projects completed
● 7 projects ongoing with
18 Nodes
● 1,5M EUR
● 4 projects completed
● 4 projects ongoing with
16 Nodes
● 0,6M EUR
● 1 project completed
● 1 project ongoing with
2 Nodes
● 0,7M EUR
● 16 projects selected for funding
● 4 projects to collaborate with
industry selected for funding
● 0,2M EUR

8. Summary of ELIXIR’s key opportunities for engagement
Core Data Resources
ELIXIR Deposition Databases
Recommended Interoperability Resources
Node Services
Service Bundles
Communities
(domain or
technology specific)
Platforms
(cross-domain,
focusing on one
aspect of service
delivery)
Focus groups
(Topic specific, open to
all)
Services

9. Sustaining Europe’s life science data infrastructure
• Mission: drive long-term sustainability
of life science data resources
• ELIXIR Core Data Resources and
deposition databases - Resources of
fundamental importance for the
research community and the long-term
preservation of life-science data.
• Basis for policy actions
• Basis for technical actions
• Capacity building
• Life cycle management
https://elixir-europe.org/core-data-resources
https://elixir-europe.org/recommended-deposition-databases

10. Resources to make data FAIR
• ELIXIR’s Recommended Interoperability
Resources.
• These are resources that:
• Establish connections between resources
• Acquire and expose metadata of different
resources
• Create the infrastructure needed to build
integratable data collections
• They will help you translate your data
across databases or resources or find the
best standards for your data.

11. Developing a tools ecosystem
Raise software
quality and
sustainability,
by producing
and promoting
software best
practices and
developing
training
activities
Bio.tools, a
discovery portal
for
bioinformatics
software
information,
providing
curated
description of
tools and data
services
OpenEBench,
an infrastructure
providing
services for
hosting
scientific
benchmark
activities and
technical
monitoring of
bioinformatics
tools and
service
To support
efforts around
software
packaging &
containers, e.g.
BioConda/
BioContainer
and support
sustainable
integration into
bio.tools and
OpenEBench
T
To drive the
development of
execution
platforms (eg
Galaxy) and
ensure
integration with
bio.tools,
OpenEBench
and workflows
using CWL
Tools Interoperability, guidelines and resources for guaranteeing platforms integration at the ELIXIR Tools
platform ecosystem, with other platforms at ELIXIR and beyond.

12. ELIXIR Training Portal
• Need to find training courses or
materials?
• ELIXIR’s TeSS Platform enables
you to search, share & package
training resources, training
materials and events
• Any content providers can
upload and include training
courses or content
Search for events held near you...
https://tess.elixir-europe.org

13. FAIR service framework
Ontologies,
formats, reporting
guidelines,
Identifier
Authorities
Metadata
Annotation
& Validation
Citation
Harvesting,
Indexing,
Search
Ontology
Mapping
Identifier
Mapping
Ontology
Lookup
Identifier
resolution
Ontology
Management
Identifier
minting
Standards &
databases
Ontologies Tools Workflows
Identifiers
Registries
Type specific
Mapping &
resolution
Extract-
Transform-Load
APIs
Standards
Services Type specific KBs,
integration &
aggregation
Knowledge

14. IMI2 project guidelines for
open access to publications
and research data
Recommended by
European funders
FAIR service framework: focus on two resources

15. Guides consumers to discover, select and use these resources with confidence
Helps producers to make their resources more visible, more widely adopted and cited
FAIRsharing: promotes use and value of databases, standards, policies
Total of
over 3584 resources
(Feb 2022)
repositories
standards
policies

16. FAIRsharing: an informative, educational resource, and a service
Provides curated descriptions and relationship graphs of
standards, databases and policies in all disciplines
COMMUNITY STANDARDS
DATA POLICIES
by funders, journals
and other organizations
DATABASES
including repositories
and knowledgebases
Identifiers
Terminologies Guidelines
Formats

17. FAIRsharing: the work of an international collective
Examples of users, adopters, collaborators and contributors:
An endorsed output of the
FAIRsharing WG
(since 2015):
A WG (since 2015) in:
Researchers in academia,
industry and government
Developers & curators of
resources and tools
Research data facilitators,
librarians, trainers
Society, unions
and community alliances
Journal publishers and
organisations with data
policies
Funders and data
policy makers
A recommended resource in EOSC reports
Used by all stakeholder groups
https://fairsharing.org/communities

18. Turning knowledge into recipes
Recipe summary card, examples:

19. Step by step process
Guidelines, process,
description
References
What should I read next?
Ingredients
An idea of tools/skills needed
Examples
Practical
elements, code
snippets
#Python3
#zooma-annotator-script.py
file
def
get_annotations(propertyTy
pe, propertyValues, filters =
""): "””
Get Zooma annotations for
the values of a given
property of a given type.
""”
import requests
annotations = []
no_annotations = []
A resource for FAIR doers

20. https://doi.org/10.1038/s41597-019-0286-0
Applied examples: these are key!

21. Editorial Board and +50 life sciences professionals and data managers
FARIplus
partners
Industry
+
Academia
ELIXIR
Nodes
represented
Creators and contributors
fairplus-cookbook@elixir-europe.org
(current) https://fairplus.github.io/the-fair-cookbook
(soon!!) https://faircookbook.elixir-europe.org

22. A live ever-growing resource:
become part of a community of FAIR experts!
1Identify a chapter and a topic
Findability Accessibility Interoperability Reusability
Infrastructure Applied examples Assessment
2 Choose a way of contributing and see our guidelines
Google Docs
HackMD
Git
Markdown cheat sheet
Get recipe template
Tips and tricks
Submit an
outline
3
You can
discuss it
with the
Editorial
Board

24. FAIRification is a team sport...
...it takes a village…

25. Impact: assessing the value of pan-European coordination
• Can be understood as ‘synergy’ or ‘economy of scale’
• In the context of ELIXIR = the cooperation of 220 organisations!
• A challenge specific to
ELIXIR due to its distributed
and international nature
• Impact of our Commissioned
Services, in connecting Nodes and
reducing fragmentation of effort
• Other challenges: measuring
the value and impact of
interoperability (efficiency savings),
of ELIXIR “badges”(e.g. Core Data
Resources),...

26. Impact example: BioHackathon
(latest 2021 in Barcelona)
• 38 Projects accepted
• 4 run totally virtual
• 3 industry led (ATOS, Owkin and DNAnexus)
• 30 hybrid projects
• 435 participants registered for the event
• 154 attending F2F meeting La Mola, Barcelona
• 281 attending virtually
• Using Remo, Zoom and Owl cameras to enhance
hybrid experience
• Encouraging project leads to submit BioHackrXiv
report at the end of the Hackathon

27. Impact example: BioHackathon Post-event survey + back-of-the-envelope calculation
ELIXIR Biohackathon 2019:
● Acceleration towards outcomes by a factor of 3 to 5
● “I would never be able to achieve the same outcome without the help
received during the event” ⎯ 16 % of respondents (N = 111 respondents)

28. BioHackathon
Personal outcomes of 111
participants (2019)

29. www.elixir-europe.org
Thank you!