A European Infrastructure for Biological Information

A European Infrastructure for Biological Information

Genome EmbryoCell

Fruitfly

Protein

Mouse Human Development,

Ageing, Disease

www.elixir-europe.org

http://www.elixir-europe.org/

ELIXIR MissionTo construct and operate a sustainable infrastructure

for biological information in Europe, to support life science research and its translation to medicine and the environment, the bio-industries and society.

• Partners: 32 partners, 13 member states• Funding: 4.5 M€ from EU FP7 • Deliverable: Consortium agreement to define the

scope of the infrastructure and how it will be constructed

Goals for ELIXIR

• Optimal Data Management• Coordinated Data Resources with improved access• Integration and interoperability of diverse heterogeneous data• Good Value for Money

• Forge Links to data in other related domains

• A single European voice in international collaborations to influence global decisions and maintain open access to data

• Enhance European competitiveness in bioscience industries

• Address need for Increased Funding & its Coordination

ELIXIR: a sustainable infrastructure for biological information in Europe. 4

Stakeholders

• Funders of Infrastructure– National Government Funding Bodies; EMBL; EU

Charities; Industry

• Data Resource Providers – Core Resources– Specialist (Many investigators - distributed)

• Data Providers– Experimentalists

• Tool Providers– Bioinformatics Groups

• Users

Why do we need ELIXIR?

•Data Growth

•Global context

•Very large user community: • 3.3 m web hits/day

• 20,000 unique users per day

•Need to preserve data and make accessible to all

•Impact on medicine & agriculture

•Impact on society & bioindustries

•Need for increased funding for biodata resources

Server Storage

0200400600800

100012001400

2006 time now

TB

Europe

USA

Japan

Good Value for Money e.g. PDB

Data collectionIn 2008

Annual Cost of PDB

ME

uro

<1%


The Preparatory Phase project

Two phases:– Committee meetings of stakeholders to achieve

consensus and make recommendations• Jan 2008 – July 2009 NOW!• Define scope and remit of ELIXIR

– Documentation and negotiation phase• July 2009 – Dec 2010• Develop ‘International Consortium Agreement’• Define funding and legal model


1. Project management2. Data providers3. User communities4. Organisation and Legal5. Funding6. Physical infrastructure7. Data interoperability

8. Literature9. Healthcare10. Chemistry, Plants, Agriculture &

Environment 11. Training12. Tools integration13. Feasibility studies14. Reporting and negotiation

Elixir is organised into 14 work packages which have committees of (mainly) European experts associated with them.

The Preparatory Phase project

ELIXIR: a sustainable infrastructure for biological information in Europe.

ELIXIR Scientific and technical Structure

ELIXIR Council

ELIXIRNode 4

ELIXIRNode 1(EMBL-EBI)

ELIXIRNode 3

ELIXIRNode 2

ELIXIRMember States EMBL

ELIXIR ExecutiveManagement (at EMBL-EBI)

Scientific Advisory & GrantCommittee

WP4: ELIXIR Legal and Governance

Heads of ELIXIR Nodes Committee

ELIXIR Secretariat

ELIXIR Council

ELIXIRNode 4

ELIXIRNode 1(EMBL-EBI)

ELIXIRNode 3

ELIXIRNode 2

ELIXIRMember States EMBL

ELIXIR ExecutiveManagement (at EMBL-EBI)

Scientific Advisory & GrantCommittee

ELIXIR Governance

Heads of ELIXIR Nodes Committee

ELIXIR Secretariat

ELIXIR


ELIXIR‘s tasks

What will ELIXIR provide?

• Core and Specialist data resources

• Compute Centres

• Services for the user community


What are the responsibilities of the ELIXIR hub?

• Coordinate and support ELIXIR activities in Europe• Quality control and organisation of selection process

(peer review) for new nodes?• Provide core data resources• Host main data centre• Ensure back up of core data resources• Training and dissemination


ELIXIR Nodes – basic description

• Prerequisites:– National or international legal entity or represented by legal

entity– Capable of entering into contract with ELIXIR Hub– Provide additional funding sources (matching funds)– Capable of supporting one or more components of ELIXIR

Infrastructure, e.g. of scientific or technical nature– ELIXIR components must have European service dimension– Other requirements to be determined (e.g. size, quality)

• Selection and application process to be decided (e.g. calls for proposals)


What are the attributes of ELIXIR nodes?

- scientific excellence - fit of thematic area - reliability- service-mentality- coordinator of national activities?- national contact point for ELIXIR- availability of funding (50-100%)- multi-year commitment (min. 5 years)- supported by host country government- subject to regular reviews- participation in software and standards development


Resources needed for ELIXIR nodes

- Staff (incl. technical support staff)- Buildings- Equipment: computers- Payment of subscriptions (eg for databases) and other

fees for specialised services- Participation in software development projects- Participation in standards development activities


WP5 Activities: Funding

• Engaging European research funders– Initial identification of funders’ aims and priorities – 2008 Survey– 3 meetings of WP5 Committee – Ongoing process of dialogue (& advocacy)

• Working with Work Package 4 to develop ELIXIR model– Identify feasibility and acceptability for funders

• UK Large Facilities Capital Fund support– Develop case for additional data storage facilities for EBI and supporting UK HTP

sequencing activities

WP2: Data Providers Recommendations

PRINCIPLES:• Data sharing is the norm in the biomolecular domain -

– Public domain principles (can this be consistent with industry funding?)– Data should be downloadable in their entirety

• Collaboration and avoidance of duplication in core data archives essential– Data bases produced by research with primary responsibilities only to

their research group are not Elixir

• Creative competition on services desirable

• Global context

• Standardisation

Databases: molecules to systems

GenomesEnsembl, Ensembl

Genomes, EGA

GenomesEnsembl, Ensembl

Genomes, EGA

Nucleotide sequenceEMBL-Bank

Nucleotide sequenceEMBL-Bank

Gene expressionArrayExpress

Gene expressionArrayExpress

ProteomesUniProt, PRIDE

ProteomesUniProt, PRIDE

Protein families, motifs and domains

InterPro

Protein families, motifs and domains

InterPro

Protein structurePDBe

Protein structurePDBe

Protein interactionsIntAct

Protein interactionsIntAct

Chemical entitiesChEBI, ChEMBL

Chemical entitiesChEBI, ChEMBL

PathwaysReactome

PathwaysReactome

SystemsBioModelsSystemsBioModels

Literature and ontologiesCitExplore, GO

Literature and ontologiesCitExplore, GO

531 Databases surveyed

208 Responded, 323 did not

Alive, 390

Dead, 63

Unclear, 78

Dead = no update since 2005

Total European effort• 200 Databases• 700 People• 100 Institutions• 60 million web hits per month• Total investment to date €308 million• Annual cost €35 million

BUT• About 1/3 of responders report NO costs• 60% of polled databases didn’t respond

– It is almost certain that the non-responders are smaller on average

RECOMMENDATIONCoordination and prioritisation, as well as stable funding, is needed for many of these resources

Security of the databases (out of 208)

Not assured, 60

Assured for at least 1 year, 51

Assured for at least 3 years, 43

We are considering commercialisation, 1

Assured for more than 5 years, 6

Assured for at least 5 years, 4


WP3: User Communities

• User Survey: 800 responses– Long term support essential– Top 3 challenges:

• Data integration; Format compatability; Website usability– Concerns

• Data quality and measures; Quality of tools;Training

• Need to consider different needs in different countries• Need for a plan for long-term maintenance of computational tools

– Create mechanisms for long-term maintenance of bioinformatics tools • user-friendly & machine-friendly interfaces

• Need for standards for formats and integration– Increased integration of databases, tools and between infrastructure domains

• Need to provide mechanisms for prioritisation of need for resources

ELIXIR WP12 Committee meeting, November 2008Søren Brunak

WP12 Tool integration priorities

• Short term:– Access: Programatic access, (traditional clickable interfaces,

downloads)– Basic infrastructure should work from the start in order to take off– Not new webservice technologies – winning ones largely identified*– Focus on accessibility, uptime, replication, testing and user scope– Well-maintained catalogs– Benchmarking frameworks (including maintenance)

• Medium term:– User category-sensitive aspects– Recommended hardware for WSs– Advanced benchmarking and tool comparison– Tool termination policies

• Long term:

– End-user data and tool integration– Commercial tools adopt standards defined by public effort

(long term goals hard to obtain from industry in particular big pharma)

ELIXIR WP12 Committee meeting, November 2008Søren Brunak

Elixir Tool integration marketing bait

”Parsed on arrival”


WP8: Literature

Europe will greatly benefit from a pan-European open access repository for scientific articles and related relevant text resources., interlinked with the other core data resources and embedded in text processing environments.

ELIXIR should enable and maintain an infrastructure for the biomedical research community that:

1) brings together textual resources from different origins, 2) integrates the text resources into the biological databases, 3) allows efficient exploitation of the resources with automatic and

interactive means and 4) supports formatting and semantics standards, to support scientific

progress for the whole bio-med-chemical research community.


WP9: Healthcare Recommendations

• Elixir should be a valuable resource for Healthcare– Contribute to translational, clinical research– Close collaboration with related infrastructures (e.g., biobanks,

imaging, population-based registries/databases/trials)

• Elixir must– Address the challenge of heterogeneous, often poorly structured data– develop and maintain nomenclatures and ontologies– support development of processing different data e.g. text & images)– include requirements from related domains (e.g., privacy protection)– facilitate communication with related domains (e.g., import and export of

data, storing of meta data)– explicitly assign the responsibility to continuously and actively seek

collaboration to certain partners or nodes to ensure accountability and transparency.


WP 10: Chemistry, Plants, Agriculture & Environment

• Support / extend current core resources for – Nucleotide/protein sequence, genomes, structures, interactions etc.

• Selected specialist resources migrated to Elixir infrastructure– Reduce complexity of informatics landscape, maintain functionality– Integration allows mining of combined data

• Adopt key data standards and work for common infrastructure– Link to other ESFRI, non ESFRI European projects– Link to non European initiatives (NSF/iPlant, DOE/Camera)

• Free access to Elixir data and core analysis tools– Web based queries, programmatic access, download


WP11: Training

Identified training issues in Europe:• Little or no coordination• Rapid evolution of bioinformatics resources• Lack of a centralised body for guidance;• Lack of recognition of the importance of bioinformatics user training,

even within the bioinformatics community.

Elixir recommendations:Link the development of data resources to the provision of trainingmaterials;Create a training support unit that will: a) provide a centralised training registry;b) provide support for trainers throughout Europe

c) develop benchmarking and evaluation systems; d) provide mechanisms for developing new training programmese) act as a single point of contact for national and pan-European training


ESFRI Biology Research Infrastructure proposals.

BBMRI(Biobanking)

INSTRUCT(Structural biology)

ELIXIR

Infrafrontier(Mouse)

ECRIN(Clinical Trials)(Translational Research)

EATRIS

(Biological Information)

Target ID Hit Lead Lead Opt Preclinical Phase I Phase II Phase IIITarget Val

Research Discovery Development


Many meetings!!

Versailles 9 December 2008ECRI 2008. European Conference on Research Infrastructure

Nancy 21 November 2008L’Institut de l’Information Scientifique et TechniqueLaunch of Standards-based Infrastructure with Distributed Resources (SIDR)

Paris 21st & 22nd Octobere-IRG open workshop organized by GIP RENATER under the French EU-presidency Information exchange between the ESFRI PPPs & the e-Infrastructure Community

Bergen October 9-101) Norwegian Bioinformatics Forum 2) Meeting with Stakeholders & Research CouncilMake case for Norwegian Involvement in ELIXIR

Innsbruck, 1-4 Oct 2008 3rd ESF Functional Genomics & Disease ConferencePresentation at BIOSAPIENS symposium

11th-12th September 2008, Duesseldorf, GermanyERASysBio 2nd Meeting of European Systems Biology CentresPresentation on ELIXIR SB Feasibility Study

Edinburgh 8-11th Septembere-Science All hands Meeting Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructures

Munich 20th AugustPARADE partners planning meetingPresentation on EBI contribution to PARADE

Helsinki 11 AugustFinnish Stakeholders MeetingMake case for Finnish involvement in ELIXIR

9th of July in LisbonFirst meeting of national network of bioinformatics Presentation and meet with government representatives

July 4th in Rome.Meeting of the BITS (Bioinformatics Italian Society)Perspectives of Bioinformatics in Europe (e.g. Elixir project, etc.).


ELIXIR evolution

Nov 2007

Prep. Phase Interim Phase Permanent Phase

Dec 2010

Dec 2021Dec 2011

Dec 2016

Dec 2016

ELIXIR

EMBL Indicative Scheme

Dec 2020Dec 2013

EU Framework Programme 7 EU FP8


Next Steps

• On course to produce reports from all surveys and WPs by mid July

• Many visits to member countries are ‘in progress’ – to identify unique contributions and requirements

• Further discussions needed with international colleagues

• THEN – discussions on International Consortium Agreement and Funding

Benefits of ELIXIRThis infrastructure will contribute to European science by:• Optimising access and exploitation of life-science data.

• Ensuring longevity of the data and protecting investments already made in research which collected the data,

• Increasing the competence and size of the already-large user community by strengthening national efforts in training and outreach.

• Enhance the global success and influence of Europe in life-science research and industry.

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A European Infrastructure for Biological Information

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