sharing data from clinical and medical research
TRANSCRIPT
Sharing data from clinical and medical research
Christoph Steinbeck
European Bioinformatics Institute(EMBL-EBI)
Post Genomic Era
Christoph Steinbeck
European Bioinformatics Institute(EMBL-EBI)
[O]ur understanding of the human genome has changed in the most fundamental ways. The small number of genes -- some 30,000 -- supports the notion that we are not hard wired. We now know the notion that one gene leads to one protein, and perhaps one disease, is false.
Craig Venter, June 2001
Genes are not the full story
Nutrition
Exercise
Disease
AgeDrugs
Environment
Phenome/ Exposome
The Metabolome is the most accessible and
dynamically changing Molecular Phenotype
Investigating Metabolomes at Large Scale
to disentangle the exposome conundrum
Phenome Centres popping up all over the world
• London
• Birmingham
• Shanghai
• United States NIH RCMRCs
• …
Time Scales: Patient Journey vs Population Modelling
> 100,000 patient samples / year> Several PetaBytes/year
=> ExaBytes of human data at moderate scale-up
Open BioData Sharing
• OpenGenomes.org
• Commercial community efforts (23AndMe …)
• Quantified-Self revolution
• Individual efforts
• Apple health kit
• Who will write the FaceBook for Personal Medical Data?
23AndPee
MetaboLights
http://www.ebi.ac.uk/metabolights
open-access, cross-species, cross-application,long-term supported
Salek, R.M., Haug, K. and Steinbeck, C. (2013) Dissemination of metabolomics results: role of MetaboLights and COSMOS. Gigascience, 2:8.
MetaboLights Database
Experimental Repository
Reference Layer
Chemistry Spectroscopy Biology
Ana
lysi
s To
ols
Primary Literature
Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
Controlled VocabulariesOntologies
Minimum Information Standards
Data growth in EBI data repositories
3-month doubling time
for Metabolomics
MetaboLights is now the recommended repositoryfor the Nature journals,
EMBO journal, PLOS journals, Metabolomics
Journal and others
Global Collaboration in Metabolomics and the
BioSciences
COSMOS COrdination of Standards in MetabolOmicS
European FP7 coordination action coordinated by us at EMBL-EBI, Hinxton,
Cambridge
• Create missing standards & formats
• Define workflows for dissemination
• Create world-wide data network
MetabolomeXchange 2014
• Global network for exchange and discoverability of metabolomics data
• Includes study as well as reference data
- Coordination of Standards in Metabolomics
What’s next?
From Molecules to Medicine
Large scale computing with medical metabolic phenotyping data
Christoph Steinbeck and the PhenoMeNal consortium
European Bioinformatics Institute(EMBL-EBI)
PhenoMeNal: Building an e-Infrastructure for Large Scale Computing with Medical Metabolic Phenotyping Data
• EBI lead• H2020• 3 Years• 13 Partners• 8 Mio €• 830 PM• Kick-off 9/15
PhenoMeNal: Large Scale Computing with Medical Metabolic Phenotyping Data
PhenoMeNal: Large Scale Computing with Medical Metabolic Phenotyping Data
Data Sharing Issues
in Clinical Metabolomics
Data Sharing Issues in Metabolomics
Data Sharing Issues in Metabolomics
Data Sharing Issues in Metabolomics
Thanks for your attention
