Identity management – life sciences perspective Ugis Sarkans European Bioinformatics Institute
Feb 23, 2016
Identity management – life sciences perspective
Ugis Sarkans
European BioinformaticsInstitute
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European Bioinformatics Institute• Outstation of the European Molecular Biology Laboratory• International organisation created by treaty (cf CERN, ESA)• EMBL-EBI has 400 Staff, €30 Million Budget, several million
users• 15 year history of service provision and scientific excellence• Sited at the Wellcome Trust Genome Campus Hinxton,
Cambridge, UK after European competition
2008funding sources
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• To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
• To contribute to the advancement of biology through basic investigator-driven research in bioinformatics
• To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
• To help disseminate cutting-edge technologies to industry
EMBL-EBI Mission
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• Life sciences• Medicine• Agriculture• Pharmaceuticals• Biotechnology• Environment• Bio-fuels• Cosmaceuticals• Neutraceuticals• Consumer products• Personal genomes• Etc…
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
PathwaysReactomePathwaysReactome
SystemsBioModelsSystems
BioModels
Literature and ontologiesCitExplore , GO
Literature and ontologiesCitExplore , GO
Comprehensive, universal, integrated…
Challenges facing information infrastructure for life sciences
• The growth of biomedical data is faster than the Moore's law• Data generated in geographically distributed manner, but
needs to be tightly integrated for interpretation • Data analysis algorithms need to be applied to combined
datasets on raw data level • Human research subject data (clinical data) needs to be
integrated with bio-molecular data raising the privacy issues and need for highly controlled access
• The data analysis algorithms are becoming more compute intensive – the need for parallelisation
Dynamic growth response
Log(data volume)
Time
Available disk space
Dynamic growth response
Log(data volume)
Time
Data to be stored
Available disk space
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What is Elixir?
• An EU Framework 7 Preparatory Phase Project• Coordinated by Prof Janet Thornton, Director EMBL-EBI• To construct a plan for the operation of a sustainable
infrastructure for biological information in Europe• €4.5 million grant awarded May 2007, three year term• 32 member consortium engaging many of Europe’s main
bioinformatics funding agencies and research institutes• Deliverables are memoranda of understanding to fund the
implementation phase which could cost €500 million • Interested parties should register as stake-holders via the
ELIXIR Website: www.elixir-europe.org
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ESFRIThe European Strategy Forum on Research Infrastructures
• Created by the Commission in February 2002• Adopted by the Competitiveness Council in April 2002• Representatives of EU Member States, Associated States, and one
representative of the European Commission. • Chairman: Prof Carlo Rizzuto (Sincrotrone Trieste S.c.p.A.-ELETTRA,
IT) • To support a coherent approach to policy-making on research
infrastructures in Europe• To act as an incubator for international negotiations about concrete
initiatives
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European Roadmap for Research Infrastructures
• 35 ‘mature’ projects for new large scale Research Infrastructures
• Based on an international peer review process• Covers all scientific areas, regardless of possible location • Likely to be realized in the next 10 to 20 years• Supported by a relevant European partnership or
intergovernmental research organisation.• Impact on science and technology development at
international level • Support new ways of doing science in Europe• Contribute to the enhancement of the European Research
Area
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Roadmap projects summary.
• 6 Social Science & Humanities• 8 Environmental Sciences• 3 Energy• 6 Biomedical and Life Sciences• 7 Material Sciences• 5 Astronomy, Astro-, Nuclear and Particle Physics
• 1 Computer and Data Treatment (transverse)
http://cordis.europa.eu/esfri/
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Cost of 35 Mature ESFRI RI Projects
Physics£3,600
Materials£4,500
Energy£2,200
Biomedical£1,600
Environment£1,300
Computing£300M
Social Science
Total Capital Cost = €13,696 Million
The ten ESFRI BMS RI
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1515
ELIXIR Scientific & Technical Structure
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BMS Support of the European Grand Challenges
ELIXIR will provide Infrastructure forthe other ESFRI BMS RI.
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BioMedBridges
• Call 8 (Research) Topic 2.3.2 “Clustering the ESFRI BMS.” • Coordinated by Janet Thornton• To create the links between the ESFRI BMS RI• €10.6M over 4 years, 21 participating organisations, 12 WP• To “build bridges” between the infrastructures• Deliverables are infrastructure components that will link data
from the different domains of the ESFRI BMS RI to ELIXIR Core Datasets
• It is anticipated that these components will be incorporated into ELIXIR Construction Phase
• ESFRI BMS RIs will be doing the work• e-Infrastructure Advisory Panel: GÉANT, DANTE, EGI.eu, PRACE
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BioMedBridges Structure of Proposal
• WP1 Management• WP2 Outreach and inreach• WP3 ESFRI BMS Standards Description and Harmonization• WP4 Technical integration• WP5 Secure access• Five Use Cases WP6 – WP12
– WP6 Interoperability of large scale image data sets from different biological scales– WP7 PhenoBridge - crossing the species bridge between mouse and human– WP8 Personalized Medicine - integrating complex data sets to understand disease
pathogenesis and improve biomarker and treatment selection– WP9 From cells to molecules - integrating structural data – WP10 Integrating disease related data and terminology from samples of different types
• WP11 Technology Watch• WP12 Training
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EMBL-EBI: Most important data collectionsGenomes & Genes
1. Ensembl: Joint project with Sanger Institute - high-quality annotation of vertebrate genomes2. Ensembl Genomes: Environment for genome data from other taxons3. 1000 Genomes: Catalogue of human variation from major World populations4. EGA*: European Genotype Archive* – genotype, phenotype and sequences from individual subjects and controls5. ENA: European Nucleotide Archive – all DNA & RNA, nextgen reads and traces
Transcription6. ArrayExpress: Archive of transcriptomics and other functional genomics data7. Expression Atlas: Differentially expressed genes in tissues, cells, disease states & treatments
Protein8. UniProt: Archive of protein sequences and functional annotation9. InterPro: Integrated resource for protein families, motifs and domains10. PRIDE: Public data repository for proteomics data11. PDBe: Protein and other macromolecular structure and function
Small molecules12. ChEBI: Chemical entities of biological interest13. ChEMBL: Bioactive compounds, drugs and drug-like molecules, properties and activities
Processes14. IntAct: Public repository for molecular interaction data15. Reactome: Biochemical pathways and reactions in human biology16. Biomodels: Mathematical models of cellular processes
Ontologies17. GO: Gene Ontology, consistent descriptions of gene products
Scientific literature18. CiteXplor: Bibliographic query system
* Requires authentication
reviewer
author
submittedmanuscript
publishedmanuscript
restricteddata
publicdata
Data supporting publication – typical lifecycle
European Genome-phenome Archive (EGA)• Primary archive for any data consented for research but not for fully public distribution
• all data must be de-identified and in accordance with the informed consent.
• Controlled access to the data
• distributed access policy:• Data Access Committee (DAC) • data release policy – data access application and data access agreement
• EGA supports only data access decisions that are based on the original informed consent
• authorized users have personal accounts in our system• access to the data requires account password• data decryption requires a separate key that must be requested and is sent off line
22HSF - 20.1.2011
EGA works with Data Access Committees (DAC)
23HSF - 20.1.2011
Authentication of FTP clientsis inherently insecure; we mayhave to require FTPS compliantclients (RFC 4217)
Secure Server
EGA provides archival encryption key andile path in the archive. This requires a secureAPI to facilitate access into the EGA master database
EGA secure layer
(3)
EGA secure layer
FTP Client
Request for whole file for download (with username/ password)
(1)
EGA verifies user and provides list of authorized list of files.
(2)
(4)Requested BAM data decrypted, andre-encrypted using client key
(5)Secure Server responds to FTP requests directly; FTP client downloads the custom-encrypted file
Mechanics of secure data access
Acknowledgements
• Andrew Lyall, ELIXIR project manager• Paul Flicek, Ilkka Lappalainen, EGA• Alvis Brazma, Functional Genomics,
BioMedBridges security