1.
EMBL-EBI Building the Database
with International Isolates
Guy Cochrane, PhD

2.
Structured
NeutralSustainable
Rapid
Data & Analysis
Requirements

3.
COMPARE
COMPARE: the enabling system for rapid identification, containment and
mitigation of emerging infectious diseases and foodborne outbreaks by
generation and comparison of genomic information on samples and
pathogens across sectors, time and locations, with additional contextual data.
A global platform for the sequence-based rapid
identification of pathogens

4.
EMBL European Bioinformatics Institute
Genes, genomes & variation
ArrayExpress
Expression Atlas
Metabolights
PRIDE
InterPro Pfam UniProt
ChEMBL ChEBI
Literature &
ontologies
Europe PubMed Central
Gene Ontology
Experimental Factor
Ontology
Molecular structures
Protein Data Bank in Europe
Electron Microscopy Data Bank
European Nucleotide
Archive
1000 Genomes
Gene, protein & metabolite expression
Protein sequences, families &
motifs
Chemical biology
Reactions, interactions &
pathways
IntAct Reactome MetaboLights
Systems
BioModels
Enzyme Portal
BioSamples
Ensembl
Ensembl Genomes
European Genome-phenome Archive
Metagenomics portal

5.
European Nucleotide Archive (ENA)
http://www.ebi.ac.uk/ena/
• Globally comprehensive scientific record and
European node of INSDC
• A broad platform for the management, sharing,
integration and dissemination of sequence data
• Established in the early 1980s, extended for new
technologies and applications
• Connectivity with broader EMBL-EBI resources
• Sequence data foundation
• Sustained within EMBL-EBI under EMBL funding
with additional support from EC, UK Research
councils, Wellcome Trust, etc.
• Substantial scale: 1.3 petabase pairs across >1
million taxa, 2,000-5,000 active data providers,
global consumer userbase
• Rich submission, discovery and retrieval
software, tools and services

6.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Structured data sharing
Data
(primary & derived)
Analysis
(routine & ad hoc)

7.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Structured data sharing
Data
(primary & derived)
Analysis
(routine & ad hoc)

8.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Structured data sharing
Data
(primary & derived)
Analysis
(routine & ad hoc)
Storage Compute

9.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Structured data sharing
Data
(primary & derived)
Analysis
(routine & ad hoc)
Storage Compute

10.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Structured data sharing
Data
(primary & derived)
Analysis
(routine & ad hoc)
Storage Compute

11.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Data Hubs
Data
(primary & derived)
Analysis
(routine & ad hoc)
Storage Compute
Data Hubs
COMPARE-VM
Notebooks

12.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Data Hubs
• Reporting and Sharing system
– Quarantined pre-publication confidential and
public data
– Set up for data providers and data consumers
– Data / metadata:
• reported through systematic reporting system Webin
– interactive and programmatic interfaces
• structured and validated
• upon release embargoed data > INSDC

13.
Data reporting

14.
Data reporting

15.
Data reporting

16.
CGE batch upload

17.
Data reporting

18.
dcc_sibelius

19.
dcc_sibelius

20.
Data access

21.
Systematic analysis

22.
Status of workflows

23.
Jupyter
Notebooks
• Live, low barrier
exploration
• http://148.6.80.191/menu.html
• https://148.6.80.191/user/dem
o/notebooks/menu.ipynb

24.
COMPARE reference genomes
GUI: http://www.ebi.ac.uk/ena/data/xref/search

25.
This project has received funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No 643476.
Data Portal
Data
(primary & derived)
Analysis
(routine & ad hoc)
Storage Compute
Data Portal

26.
People
DTU
Jose Luis Bellod Cisneros
Martin Christen Frølund Thomsen
Johanne Ahrenfeldt
Rolf Sommer Kaas
Lukasz Dariusz Dynowski
Ole Lund
Frank Aarestrup
Jeffrey Skiby
WIGNER
János Márk Szalai-Gindl
László Oroszlány
Dávid Visontai
Dezso Ribli
Istvan Csabai
EMBL-EBI
Nima Pakseresht
Clara Amid
Nicole Silvester
Marc Rossello
Neil Goodgame
Suran Jayathilaka
Ana Luisa Toribio
Ana Cerdeño Tarraga
Petra ten Hoopen
Rasko Leinonen
Guy Cochrane
EMC
Ron Fouchier
Marion Koopmans
Saskia Smits
David van de Vijver
Marjolein Poen
FLI
Martin Beer
Anne Pohlmann
Dirk Hoeper
Claudia Wylezich
Ariane Belka
APHA
Sharon Brooks
Amanda Seekings
Jill Banks
Javier Nunez
Richard Ellis
Ian Brown
SSI
Eva Litrup
Eva Møller Nielsen