# ELIXIR: the distributed infrastructure for life-science information

Anne-Françoise Adam-Blondon

<figure><img src="image_1.png" /></figure>

## To cite this version:

Anne-Françoise Adam-Blondon. ELIXIR: the distributed infrastructure for life-science information. LERU Open Science Ambassador meeting, Université Paris-Saclay, Nov 2023, Gif-sur-Yette, France. hal-04503092

HAL Id: hal-04503092

https://hal.inrae.fr/hal-04503092

Submitted on 13 Mar 2024

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

<figure><img src="image_2.png" /></figure>
<figure><img src="image_3.png" /></figure>

# ELIXIR: the distributed infrastructure for life-science information

A-F Adam-Blondon, INRAE, ELIXIR-FR Head of node

LERU Open Science Ambassadors meeting,
Université Paris-Saclay, France, 2023 Nov 9th

www.elixir-europe.org

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

@ELIXIREurope

<figure><img src="image_6.png" /></figure>

/company/elixir-europe
# ELIXIR Europe

ELIXIR is an intergovernmental organisation that brings together **life science** resources such as

- databases

- software tools

- training resources

- interoperability resources

- compute resources

- data management support

The goal of ELIXIR is to **coordinate bioinformatics resources from across Europe so they form a single infrastructure.**

<figure><img src="image_7.png" /></figure>
# ELIXIR – who we are

## 24 Nodes

* ELIXIR Nodes form national networks of excellence, containing a total of 245 institutes/universities

* EMBL-EBI is one of the nodes

## 1 Hub

The Hub, located at EMBL-EBI, Cambridge, UK, provides the secretariat and coordinating activities for ELIXIR

<figure><img src="image_8.png" /></figure>
# Enable data-driven solutions to societal challenges

Disease prevention

<figure><img src="image_9.png" /></figure>

Climate change

<figure><img src="image_10.png" /></figure>

Disease
diagnosis

<figure><img src="image_11.png" /></figure>

Pandemic
preparedness

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

People

<figure><img src="image_14.png" /></figure>

Cancer

<figure><img src="image_15.png" /></figure>

Diminishing
biodiversity

<figure><img src="image_16.png" /></figure>

Sustainable
food
production

<figure><img src="image_17.png" /></figure>

Data

<figure><img src="image_18.png" /></figure>

Science

<figure><img src="image_19.png" /></figure>

Impact of climate &
geopolitics on farming
<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

INSTITUT FRANÇAIS DE BIOINFORMATIQUE

## IFB is a distributed French National Research Infrastructure

- 36 platforms and research teams spread all over France

### Coordination: IFB-core

- Multi-research organizations : CNRS, Inserm, INRAE, CEA

### Common resources

- Supported by the French Ministry of Higher Education and Research since 2012

### A large set of expertise in bioinformatics

- >400 experts (~200 FTE)

<figure><img src="image_22.png" /></figure>
<figure><img src="image_23.png" /></figure>

IFB's domains of application encompass the three scientific priorities of the 2024-2028 programme of ELIXIR

<figure><img src="image_24.png" /></figure>

Enabling and responding to
advances in cellular and molecular
research will drive life science

Connect the latest developments and
established data resources to realise
the potential of cellular and molecular
biology

<figure><img src="image_25.png" /></figure>

Biodiversity, food security and
pathogens are interrelated
societal challenges

Mobilise and integrate molecular data
to support transnational research
programmes in biodiversity, food
security and pathogens

<figure><img src="image_26.png" /></figure>

<figure><img src="image_27.png" /></figure>

The promise of genomics
research to improve health
and disease outcomes

Provide the infrastructure to support
the discovery, access, sharing and
analysis of human genomics data and
linked data on a massive scale
* Sharing expertise and working groups on subjects of common interest

* Partnership in large national projects

* Enhance partnerships in ELIXIR activities and in European projects

<figure><img src="image_28.png" /></figure>
# How we work - ELIXIR Platforms

**Platforms** bring together experts from Nodes to develop ELIXIR's technical vision and coordinate activities in defined technical areas. There are five Platforms:

**Compute**

Builds and integrates **cloud, compute, storage and access services** for the life-science research community

**Data**

Drives the use, re-use and value of life science data by providing **curated, robust, long-term sustainable data resources** within a coordinated, scalable and connected data ecosystem

**Tools**

Helps communities **find, register and benchmark** software tools; maintains information standards and produces, adopts and promotes **best practices for tool development**

**Interoperability**

Helps people and machines to **discover, access, integrate and analyse biological data**; encourages the life science community to adopt **standardised file formats, metadata & vocabularies**

**Training**

Strengthens **national training** programmes; grows bioinformatics and research data management **training capacity and competence across Europe**; empowers researchers to use ELIXIR's resources

<figure><img src="image_29.png" /></figure>

<figure><img src="image_30.png" /></figure>

LS LOGIN

elixir
Core Data
Resource

<figure><img src="image_31.png" /></figure>

<figure><img src="image_32.png" /></figure>

<figure><img src="image_33.png" /></figure>

<figure><img src="image_34.png" /></figure>

<figure><img src="image_35.png" /></figure>
# ELIXIR Training Platform

Service/Product

• Activity

ELIXIR trains the trainers

ELIXIR nodes train the users

Train-the-trainer

TeSS

GitHub

* FAIR training material

* Train the Trainer

* Lesson template

* TeSS for material

Designing
learning
material

01

* Improve the Handbook

* Lessons learned

* Best practices

05

Feedback to
the process

Training Handbook

Learning
pathways

02

* Professional guidelines

* TeSS Learning Pathways

* FAIR material

04

Impact
assessment

* Review impact (TMD)

Training Metrics
Database - TMD

Delivery of
course

03

* Trainers network

* Code of Conduct

* Short and long term
  feedback

* Certification

* TeSS for course

TeSS

Training Resource
Certification

Training Metrics
Database - TMD

Training Handbook

TeSS
# How we work - ELIXIR Communities: connecting infrastructure & life science experts

<figure><img src="image_36.png" /></figure>

* Formed around domain experts in ELIXIR Nodes (including non-ELIXIR partners)

<figure><img src="image_37.png" /></figure>

* Provide a mechanism for long-term collaborations with other ESFRIs and large-scale initiatives

<figure><img src="image_38.png" /></figure>

* Drive service developments in the ELIXIR Platforms

<figure><img src="image_39.png" /></figure>

* Provide a framework to develop and maintain community standards

<figure><img src="image_40.png" /></figure>

The [ELIXIR Communities Handbook](#) tells you what a Community is, who can join, what the benefits are, and how Communities are structured.

<figure><img src="image_41.png" /></figure>
* Liaising and networking with all platforms and most of the communities and contributing to their activities

* Co-coordinating and contributing to the strategic planning of some of them => **France**

* Contributing to European projects: 9 since 2020

<figure><img src="image_42.png" /></figure>

Technology

## Platforms

ELIXIR Platforms bring together experts from Nodes to develop ELIXIR's technical vision and coordinate activities in defined technical areas. There are five Platforms: Data, Tools, Interoperability, Compute and Training.

<figure><img src="image_43.png" /></figure>

### Data Platform

Aims to identify key data resources across Europe and support the linkages between data and literature.

<figure><img src="image_44.png" /></figure>

### Tools Platform

Helps researchers find the best software tools to analyse their data.

<figure><img src="image_45.png" /></figure>

<figure><img src="image_46.png" /></figure>

### Compute Platform

Develops services to make it easier to store, share and analyse large datasets.

<figure><img src="image_47.png" /></figure>

### Interoperability Platform

Develops and encourages the adoption of standards to describe life science data.

<figure><img src="image_48.png" /></figure>

### Training Platform

Helps scientists and developers find the training they need, and also provides that training.

<figure><img src="image_49.png" /></figure>

Science

## Communities

<figure><img src="image_50.png" /></figure>

3D-Bioinfo

<figure><img src="image_51.png" /></figure>

Biodiversity

<figure><img src="image_52.png" /></figure>

Food and nutrition

<figure><img src="image_53.png" /></figure>

Galaxy

<figure><img src="image_54.png" /></figure>

Intrinsically Disordered Proteins

<figure><img src="image_55.png" /></figure>

Marine Metagenomics

<figure><img src="image_56.png" /></figure>

<figure><img src="image_57.png" /></figure>

Metabolomics

<figure><img src="image_58.png" /></figure>

Microbial Biotechnology

<figure><img src="image_59.png" /></figure>

Plant Sciences

litate
crop and

<figure><img src="image_60.png" /></figure>

Proteomics

<figure><img src="image_61.png" /></figure>

Single-Cell Omics

<figure><img src="image_62.png" /></figure>

Systems Biology

<figure><img src="image_63.png" /></figure>

Toxicology

<figure><img src="image_64.png" /></figure>

R

### Human Data Communities

<figure><img src="image_65.png" /></figure>

Federated Human Data

<figure><img src="image_66.png" /></figure>

Human Copy Number
Variation

<figure><img src="image_67.png" /></figure>

<figure><img src="image_68.png" /></figure>

Rare diseases

Cancer Data
(focus group)

<figure><img src="image_69.png" /></figure>
# ELIXIR'S funding model

## Node funding:

* National roadmap funding

* Competitive research grants

* EU Structural Funds or Recovery and Resilience Facility (RRF)

* Trusts and foundations

* Industry collaboration

https://elixir-europe.org/about-us/how-funded/sustainability-plan

<figure><img src="image_70.png" /></figure>

<figure><img src="image_71.png" /></figure>

<figure><img src="image_72.png" /></figure>

<figure><img src="image_73.png" /></figure>

ELIXIR Nodes

<figure><img src="image_74.png" /></figure>

ELIXIR
Hub

Commissioned
services

## External funding:

(EC funded projects: ELIXIR represented by ELIXIR Hub or by an ELIXIR Node)

* Horizon Europe

* Digital Europe

* EU4Health

## Internal funding:

Annual contribution by member states

<figure><img src="image_75.png" /></figure>

elixir
# ELIXIR's key stakeholders

<figure><img src="image_76.png" /></figure>

## ELIXIR Nodes

- 24 ELIXIR Nodes
- 245+ institutes
- 850+ scientists

<figure><img src="image_77.png" /></figure>

## Users

- Bioinformaticians
- 500,000+ life science researchers
- Users in industry

<figure><img src="image_78.png" /></figure>

## Funders & decision makers

- European Union
- National funding agencies
- ESFRI delegates
- ELIXIR Board members

<figure><img src="image_79.png" /></figure>

## Collaborators

- ESFRI RIs
- Global initiatives (GA4GH, Galaxy)
- National initiatives (Australian BioCommons, NIH)
# Collaborator example – the ELIXIR EOSC strategic vision

## ELIXIR maps to EOSC at all levels

* Throughout the EOSC Core and Interoperability frameworks

* Bidirectional relationships, with best of breed solutions being adopted by both sides

* ELIXIR Communities will over time adopt EOSC Services and become driving user communities for both organisations

<figure><img src="image_80.png" /></figure>

## ELIXIR and the EOSC Association Task Forces

### ELIXIR on Advisory Groups

* The Implementation of EOSC

* Metadata and Data Quality

* Research Careers and Curricula

* Sustaining EOSC

* Technical Challenges on EOSC

<figure><img src="image_81.png" /></figure>

## ELIXIR involvement in EOSC projects

<figure><img src="image_82.png" /></figure>

EOSC pilot
The European Open Science
Cloud for Research Pilot Project

EOSC-Pilot

<figure><img src="image_83.png" /></figure>

EOSC
CONNECTING THE EUROPEAN OPEN SCIENCE COMMUNITIES TO ADVANCE OPEN SCIENCE

EOSC-Enhance

<figure><img src="image_84.png" /></figure>

EOSC-Life

EOSC-Life

<figure><img src="image_85.png" /></figure>

EOSC Future

EOSC-Future
# ELIXIR flagship events

## BioHackathon Europe

* Bringing together bioinformaticians for **five days of hacking**

* **Five successful annual events** since 2018

* Projects to advance **open source infrastructure** for data integration to accelerate scientific innovation

* Supporting operations across ELIXIR Platforms, Communities and Focus Groups through technology implementations (e.g. **FAIR**, identifiers, metadata standards, ontologies and metadata catalogues)

<figure><img src="image_86.png" /></figure>

## Innovation and SME Forums

* Approximately **two one-day** events per year

* Providing **Small to Medium Sized Enterprises** (SMEs) the opportunity to present their innovative ideas

* Enabling companies to learn more about **current and emerging ELIXIR services**

* Forging strong links with the **local ELIXIR Node representatives** running ELIXIR services

<figure><img src="image_87.png" /></figure>

## ELIXIR Bioinformatics Industry Forum (EBIF)

* **One-day** annual event

* Discussions with industry experts around **visionary ideas, bottlenecks and solutions** to major challenges in the data-driven life science sector

* A forum for **knowledge exchange and collaboration** in the pre-competitive space

* **Networking** opportunities with bioinformatics opinion leaders, academic experts in ELIXIR and the commercial sector

<figure><img src="image_88.png" /></figure>
# ELIXIR's Code of Conduct – the principles

The Code of Conduct pertains to ELIXIR organised or funded events

1

DIVERSITY

<figure><img src="image_89.png" /></figure>

2

ACT ETHICALLY
AND WITH
INTEGRITY

<figure><img src="image_90.png" /></figure>

3

FOSTER
TRUST AND
COLLABORATION

<figure><img src="image_91.png" /></figure>

4

RESPECT
AND SHOW
COURTESY TO
EACH OTHER

<figure><img src="image_92.png" /></figure>

**We value**

each other's perspectives

**We adopt**

a zero-tolerance approach to harassment and discrimination

**We maintain**

high ethical standards

**We'll apply**

honesty and integrity in the dealing of any transgressions against the Code.

**We're committed**

to making ELIXIR events collaborative, supportive and enjoyable

**We'll ensure**

a respectful and inclusive environment

<figure><img src="image_93.png" /></figure>

<figure><img src="image_94.png" /></figure>
What we offer

<figure><img src="image_95.png" /></figure>

Guidelines

Guidelines and best practices
to help you manage life science
data, run training courses,
develop software and more.

<figure><img src="image_96.png" /></figure>

Web portals

Find the right software,
training courses, standards and
more in our interlinked portals
to life science resources.

<figure><img src="image_97.png" /></figure>

Services

Find compute services,
databases, and the full list of
resources ELIXIR coordinates.

<figure><img src="image_98.png" /></figure>

Partnerships with
Industry and SMEs

Join events and projects that
bring the private and public
sectors together.

<figure><img src="image_99.png" /></figure>

Opportunities to
work together

Join a scientific group in ELIXIR
or partner with us to apply for
EC funding.

<figure><img src="image_100.png" /></figure>

For ELIXIR members

If you work at an institute that
is part of ELIXIR, then
remember to take advantage of
the benefits ELIXIR offers.

ELIXIR coordinates the
provision of life science
services and resources,
developed and managed by
ELIXIR Nodes

The services and resources are
freely available to researchers
around the world

The services and resources
support efficient manipulation,
analysis, storage and exchange
of life science data
# Examples of ELIXIR high impact services

<figure><img src="image_101.png" /></figure>

<figure><img src="image_102.png" /></figure>

<figure><img src="image_103.png" /></figure>

<figure><img src="image_104.png" /></figure>

<figure><img src="image_105.png" /></figure>

**Life Science Login**

Authentication service

13K

Users

**FAIRsharing**

Data and metadata resource including
standards, databases and policies

1.5K

Standards

**ELIXIR TeSS**

ELIXIR's training portal

1.9K

Training
materials

**BioContainers**

Software standardisation resource

70K

Containers &
packages

**BioTools**

Registry of tools, databases and services

35K

Monthly visits
# ELIXIR research data management resources

Guidance for data stewards, project managers and researchers

## Overview of good data management practices

<figure><img src="image_106.png" /></figure>

The Research Data Management Kit (RDMkit) guides you through the whole data management life cycle and includes advice specific to your domain, your role and your country.

## Step-by-step instructions

<figure><img src="image_107.png" /></figure>

The FAIR Cookbook contains step-by-step recipes to accomplish specific data management tasks and to make your data FAIR (Findable, Accessible, Interoperable, Reusable).

## Data management plan wizard

<figure><img src="image_108.png" /></figure>

The Data Stewardship Wizard (DSW) is an online tool that guides researchers and data stewards through their data management planning.
# Research Data Management Toolkit

<figure><img src="image_109.png" /></figure>
A web-based toolkit for the
bioscience community written by
the bioscience community

RDMkit in numbers

151

<figure><img src="image_110.png" /></figure>

Contributors

The force behind RDMkit

336

<figure><img src="image_111.png" /></figure>

Tools & resources

Explained in the context of
real world problems

101

<figure><img src="image_112.png" /></figure>

Pages

Helping you with data
management

<figure><img src="image_113.png" /></figure>
# Resources for reproducible environment of analysis

bio.tools

<figure><img src="image_114.png" /></figure>

bio.tools helps you find and
select bioinformatics software
and connect it in workflows.

BioContainers

<figure><img src="image_115.png" /></figure>

Search a repository of
containerised software that
you can build into workflows.

WorkflowHub

<figure><img src="image_116.png" /></figure>

WorkflowHub

A registry for sharing and
publishing scientific
computational workflows.

FAIRsharing.org

FAIRsharing.org
∞ standards, databases, policies

FAIRsharing.org allows you to
search for databases and data
policies by aspects such as
domain, species and country.

TeSS

<figure><img src="image_117.png" /></figure>

Search for training courses,
webinars, training materials
and workflows in TeSS, ELIXIR's
training portal.

COMMENT | FOCUS

DOME: recommendations for supervised
machine learning validation in biology

DOME is a set of community-wide recommendations for reporting supervised machine learning-based analyses applied to biological studies. Broad adoption of these recommendations will help improve machine learning assessment and reproducibility.

Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, ELIXIR Machine
Learning Focus Group, Jennifer Harrow, Fotis E. Psomopoulos and Silvio C. E. Tosatto

With the steep decline in the
cost of many high-throughput
technologies, large amounts
of biological data are being generated
and made accessible to researchers.
Machine learning (ML) has come into

9,000

8,000

7,000

<figure><img src="image_118.png" /></figure>

Check for updates

<figure><img src="image_119.png" /></figure>

Check for
updates

<figure><img src="image_120.png" /></figure>

OPEN ACCESS

**Citation:** Brack P, Crowther P, Soiland-Reyes S,
Owen S, Lowe D, Williams AR, et al. (2022) Ten

TATIONAL BIOLOGY

EDITORIAL

Ten simple rules for making a software tool
 workflow-ready

Paul Brack<sup>1, ∗</sup>, Peter Crowther<sup>1, †</sup>, 2, Stian Soiland-Reyes<sup>1,3, ∗</sup>, Stuart Owen<sup>1, ‡</sup>,
Douglas Lowe<sup>1, ‡</sup>, 4, Alan R. Williams<sup>1, ‡</sup>, Quentin Groom<sup>1, §</sup>, Mathias Dillen<sup>1, §</sup>,
Frederik Coppens<sup>1, ¶</sup>, 6, 7, Björn Grüning<sup>1, §</sup>, Ignacio Eguinoa<sup>1, ¶</sup>, 6, 7, Philip Ewels<sup>1, ¶</sup>,
Carole Goble<sup>1</sup>

1 Department of Computer Science, The University of Manchester, Manchester, United Kingdom,

2 Melandra Limited, Stockport, United Kingdom, 3 Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands, 4 Research IT, IT Services, University of Manchester, Manchester, United Kingdom, 5 Meise Botanic Garden, Meise, Belgium, 6 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium, 7 VIB Center for Plant Systems Biology, Ghent, Belgium, 8 Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany, 9 Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden

* soiland-reyes@manchester.ac.uk

Introduction

In recent years, the volumes of data to be analyzed, as well as the complexity of that analysis,
across many scientific fields (from genomics through to exoplanet exploration) have increased

CIENTIFIC DATA
110110
0111101
11011110
011101110

Amended: Addendum

OPEN

T CATEGORIES

→ Research data

→ Publication

characteristics

Comment: The FAIR Guiding
Principles for scientific data
management and stewardship

Mark D. Wilkinson et al. *

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Supporting discovery through good data management

Good data management is not a goal in itself, but rather is the key conduit leading to knowledge
discovery and innovation, and to subsequent data and knowledge integration and reuse by the

10 December 2015

12 February 2016

ed: 15 March 2016
# The European COVID-19 Data Platform

Universities

<figure><img src="image_121.png" /></figure>

Research
Centres

<figure><img src="image_122.png" /></figure>

Consortia

<figure><img src="image_123.png" /></figure>

National Health Data
Infrastructures

<figure><img src="image_124.png" /></figure>

Hospitals

<figure><img src="image_125.png" /></figure>

Public Health
Laboratories

<figure><img src="image_126.png" /></figure>

Medical
Centres

<figure><img src="image_127.png" /></figure>

Publications

Genomic sequences

Protein structures

Protein sequences

Expression datasets

Drug targets

Chemical compounds

<figure><img src="image_128.png" /></figure>

Viral data

SARS-CoV-2
Data Hubs

Human/
clinical data

Federated EGA

<figure><img src="image_129.png" /></figure>

<figure><img src="image_130.png" /></figure>

ChEMBL

<figure><img src="image_131.png" /></figure>

PDBe-KB

<figure><img src="image_132.png" /></figure>

EMDB

<figure><img src="image_133.png" /></figure>

Reactome

<figure><img src="image_134.png" /></figure>

e!
Ensembl

<figure><img src="image_135.png" /></figure>

Europe
PMC

<figure><img src="image_136.png" /></figure>

<figure><img src="image_137.png" /></figure>

InterPro

<figure><img src="image_138.png" /></figure>

PDBe

<figure><img src="image_139.png" /></figure>

EGA

<figure><img src="image_140.png" /></figure>

PRIDE

ENA

UniProt

● Open research data

<figure><img src="image_141.png" /></figure>

**COVID-19**
**Data Portal**

<figure><img src="image_142.png" /></figure>

● Access-controlled data

<figure><img src="image_143.png" /></figure>
<figure><img src="image_144.png" /><figcaption>Guy Perrière
ELIXIR-FR Head of Node</figcaption></figure>

<figure><img src="image_145.png" /><figcaption>Anne-Françoise Adam-Blondon
ELIXIR-FR Head of Node</figcaption></figure>

<figure><img src="image_146.png" /><figcaption>Angela Sáenz
ELIXIR-FR Node coordinator</figcaption></figure>