ELIXIR - dtls.nl · Experimental data Downstream analysis Clinical/Biobank Procedures Imaging...
Transcript of ELIXIR - dtls.nl · Experimental data Downstream analysis Clinical/Biobank Procedures Imaging...
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: [email protected]
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/