elixir europe · elixir europe. andrew smith, head of external relations. personalized nutrition...

www.elixir-europe.org

ELIXIR EuropeAndrew Smith, Head of External Relations

Personalized Nutrition for Better Health, Brussels 10-11 Oct 2017

Public data infrastructure for microbiome, food and nutrition research: facilitating research and innovation in the era of big data

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1. Data challenges/barriers

2. Opportunities for data-driven innovation

3. Role of coordinated public data infrastructures as part of the solution

Themes of talk

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Source: http://omicsmaps.com

• Computer speed and storage capacity is doubling every 18 months and this rate is steady

• DNA sequence data is doubling every 6-8 months over the last 3 years and looks to continue for this decade

Data growth challenge

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Source: http://omicsmaps.com

• Data production sites increasing across Europe

• Rapid emergence of new technologies: image data, proteomics, metabolomics…

Data distribution challenge

Diversity of data resources in life science

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2012. MY Galperin, GR Cochrane – Nucleic Acids Research, 2011

~1800molecular biology

data resources

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• Secure access and governance of human data

• Data often cannot transfer the boundary in which it was generated

• National/regional health systems of vary between regions, languages, providers and technologies

Data security, ethical and legal challenges

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Open data mandates

Human capital – skills development

• EC estimates 500,000 life scientists in Europe

• wet lab biologists, bioinformaticians to lab technicians….

• Need for ‘user’ training is high

• High level Expert Group on EOSC estimates Europe needs 500,000 ’data scientists’

• Need for training for data scientists and bioinformaticians

Global commodity of users

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Kafkas S, Kim JH, and McEntyre JR Database Citation in Full Text Articles (May 2013) PLoS One 10.1371/journal.pone.0063184

European Nucleotide Archive

Protein Data Bank

DNA Variations (SNPs)

Gene Expression Studies DOIs (long tail)

Data citation in Europe PMC full text articles

Data-driven innovation - demonstrating impact

*Bousfield D, McEntyre J, et al. Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. F1000Research 2016

Public data resources as a business model for SMEs

Customisation Aggregation Brokerage

Interaction with public data resources

• ELIXIR on the ESFRI roadmap

• ELIXIR one of three prioritised Research Infrastructures

• ELIXIR defined by GSO as infrastructure with global reach

Aligning national, European and global priorities

"ELIXIR is nominated because it is a world-leading infrastructure, vital for enabling the life sciences to derive maximum knowledge and understanding from biological, medical and environmental 'Big Data'.”

Group of Senior Officials on Global Research Infrastructures Progress Report 2015, October 2015

Other ESFRI Research Infrastructures

• BBMRI – biobanks • EATRIS – translational

medicine• ECRIN – clinical trials• INSTRUCT – structural

biology• INFRAFRONTIER – mouse

models

• EMBRC – marine platforms• EuroBioImaging – medical

and biological imaging • EU-OpenScreen – chemical

screening• MIRRI – microbial resources• ISBE – systems biology • EMPHASIS – plant

phenotyping

Others for Food and Health?

ELIXIR Structure

Five technical platforms for Compute, Data, Tools and Interoperability

Complemented by Use Cases for Marine meta-genomics, Rare diseases, Human data, Plants sciences,

PROTEOMICS

METABOLOMICS

GALAXY

and galaxyproteomics,

metabolomics

ELIXIR Services

Data deposition:ENA, EGA, PDBe, EuropePMC, …

Bioinformatics tools:Bio.tools

Data Interoperability:Standards,Identifiers, Ontologies

Compute:Secure data transfer, cloud computing, AAI

Industry:Innovation and SME programmeBespoke collaborations

Training:TeSS, Data Carpentry, eLearning

Data management:Genome annotationData management plans

Added value data:UniProt, Ensembl, OrphaNet, …

Recommended Deposition Databases

• “Whenever possible, biological research data should be submitted to the recommended community deposition databases”

https://elixir-europe.org/platforms/data/elixir-deposition-databases

BioTools: portal for software and analysis tools

https://bio.tools

Connecting users with specialist training

ELIXIR Training portal (TeSS)

• 230 upcoming events

• 650 online training materials

• 38 content providers

• https://tess.elixir-uk.org/

‘Local’ EGA

• Sensitive data are stored locally

• EGA provides the software platform

• First prototype in 2017 with national partners

Industry engagement

www.elixir-europe.org

@ELIXIREurope /company/elixir-europe

Thanks!