www.elixir-europe.org

ELIXIR Update on ELIXIR - TraIT pilot

Sanne Abeln (VU / ELIXIR Netherland)

ELIXIR Human Data Implementation Study 2016

Project / Study Partners Comment

ELIXIR / GA4GH Beacons

Leads: Jordi Rambla & Ilkka

Lappalainen

CRG (ES), EMBL-EBI, FR, BE,

SE, FI, NL

Implement Beacons in ELIXIR

Nodes (12M)

ELIXIR / GA4GH Metadata API

Leads: Michael Baudis & Helen

Parkinson

SIB (CH), EMBL-EBI, FR Reference implementation of

meta-data API (12M)

ELIXIR / IMI Oncotrack

Lead: Susanna Repo, David

Henderson & Dylan Spalding

Hub, EMBL-EBI, CRG (ES) Scoping study on long term data

management (6M)

ELIXIR / TrAIT: EGA backend for

TranSMART

Leads: Sanne Abeln & Dylan

Spalding

NL, EMBL-EBI, CRG (ES) Provide EGA connector for data

submission/retrieval (12M)

Human data: experimental molecular profiling

Privacy & Ethical Issues: human data

• triangle indicates average expected risk (given age, sex, etc)

• yellow line indicates risk given SNV profiles

high cholesterol

diabetes

skin cancer

increased risks:

Sequence

Variants

Phenotypes

Structural variants

Open & public archives

European Nucleotide Archive

EVA European Variation Archive

BioSamples

Database of Genomic Variants archive

Controlled access archive

Array

About the EGA: What is controlled access data?

Size of the (raw) data

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

petabyte

Molecular Profiling Data (TraIT)

raw data

processed data

computational

workflows

TraIT

Aim: “The CTMM Translational Research IT (TraIT) project is

developing and implementing a long-lasting IT infrastructure for

translational research projects in the Netherlands that will

facilitate the collection, storage, analysis, and archiving of data

generated in the biomedical research projects.”

• no research

• end-user driven

CTMM-TraIT

Five data

generation work

packages

Integration and

analysis across

the platforms

7

TraIT - Structure

wet-lab-person

tech-operator

(bio)informatician

PI / (end)user

PI / (end)user

Aim of pilot: ELIXIR-TraIT

processed data

computational

workflows

raw data

Scientific Output

Participant/ patient enters

Intellectual Property

Improved Healthcare

Experimental data

Downstream analysis

Clinical/Biobank Procedures

Imaging Samples Experiments Questionnaire

EHR

Data Integration

External data

Image database & analysis

Biobank database

Phenotype database

Participant Interaction

TraIT workflow Mostly open source IT tools

supported by international

public and private communities

8

25

26

77

human data

clinical data

experimental

profiling data

processing

workflows

sequencing

workflow

arrays

workflow

Proteomics

workflow

clinical and

processed data

archival storage

workflows &

analysis

Galaxy

transSMART

raw data storage

retrieve raw data

workflow provenance

Reference to raw data

EGA

reference workflows

human data

clinical data

experimental

profiling data

processing

workflows

sequencing

workflow

arrays

workflow

Proteomics

workflow

clinical and

processed data

...

archival storage

EGA

local storage

workflows &

analysis

Galaxy

transSMART

raw data storage

retrieve raw data

workflow provenance

Reference to raw data

Demo: TraIT - Cell Line Use Case

• Non-privacy sensitive data (cell lines)

• Test and develop workflows

• Demo and training of workflows

Try to make a general framework

Feedback needed from all of you!

collected experimental data

EMBL- EBI

• ‘European Node’

• EMBL-ELIXIR Work Programme agreed, ie, Ensembl, EGA, ENA, PDBe, EuropePMC

• Lead EXCELERATE Use Cases on Rare Diseases, Human Data, Plant Sciences, Marine..

• Involved in several ELIXIR Pilot Actions

16

ELIXIR Netherlands

• Led by DTL

• Exists as a PPP

• Officially launched in 2014

• Run Bring Your Own Data (BYOD) programme

• Large role in interoperability backbone, ie FAIR

17

ELIXIR Spain

• Long history of national collaboration - INB

• ELIXIR Pilot on EGA as a Joint Venture

• Involvement in ENCODE, ICGC, IRDiRC, RD-Connect, tomato genome consortium, various IMI projects

18

EGA Team

Paul Flicek Arcadi

Navarro

Helen

Parkinson Dylan Spalding Jordi Rambla

Angel

Carreno

Jeff Almeida-

King

Sabela de la

Torre Saif Ur

Rehman

Oscar Martinez

Pablo Garcia Mario Alberich Alexander Senf Alfred Gil Giselle Kerry

Mauricio

Moldes

Jag Kandasamy Audald Lloret

TraIT (WP4)

Remond Fijneman

Sanne Abeln

Stef van Lieshout

Mariska Bierkens

Freek de Bruijn

Thang Pham

Youri Hoogstrate

Saskia Hiltemann

TraIT

Gerrit Meijer

Jan-Willem Boiten

Wim van der Linden

Rita Azevedo

Jeroen Beliën

Pieter Neerincx

Jaap Heringa

The Hyve

Kees van Bochove

Ward Weistra

Ruslan Forostianov

Peter Kok

contact: j.bijlard@vu.nl

TraIT –WP4 (NL)

Remond Fijneman (NKI)

Stef van Lieshout (VUmc)

Mariska Bierkens (NKI)

Freek de Bruijn (NKI)

Youri Hoogstrate (EMC)

Saskia Hiltemann (EMC)

Thang Pham (VUmc)

Andrew Stubs (EMC)

Bauke Ylstra (VUmc)

Christian Rausch (NKI)

Connie Jimenez (VUmc)

Guido Jenster (EMC)

Pieter Neerincx (UMCG)

The Hyve (NL)

Kees van Bochove

Ward Weistra

Ruslan Forostianov

Peter Kok

Jochem Bijlard

Wibo Pipping

TraIT (NL)

Gerrit Meijer (NKI)

Jan-Willem Boiten (CTMM)

Wim van der Linden (Philips)

Rita Azevado (eScience/ CTMM)

Jeroen Beliën (VUmc)

Jaap Heringa (VU)

`

ELIXIR – Human Data

Dylan Spalding (EGA, EBI, UK)

Jordi Rambla (EGA, CRG, ES)

Justin Paschall (EGA, EBI, UK)

Alexander Senf (EGA, EBI, UK)

David van Enckevort (BBMRI,UMCG, NL)

Morris Swertz (BBMRI,UMCG, NL)

Luiz Bonino (ELIXIR, DTL, NL)

Susanna Repo (ELIXIR, EBI, UK)

Christine Staiger (SurfSara, NL)

Irene Nooren (SurfSara,NL)

Ilkka Lappalainen(ELIXIR)

Chao Zhang [Cico] (ADS, VU, NL)

www.elixir-europe.org

@ELIXIREurope /company/elixir-europe

THANK YOU!

Dedicated ELIXIR Track

3-7 September 2016 http://www.eccb2016.org/