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IRIDA: Canada’s federated platform for genomic epidemiology, ABPHM 2015 WHsiao
1. IRIDA: Canada’s federated platform
for genomic epidemiology
William Hsiao, Ph.D.
William.hsiao@bccdc.ca
@wlhsiao
BC Public Health Microbiology and Reference Laboratory
and University of British Columbia
ABPHM 2015
2. Genome Canada Bioinformatics Competition: Large-Scale Project
“A Federated Bioinformatics Platform for
Public Health Microbial Genomics”
Our Goal
The IRIDA platform
(Integrated Rapid Infectious Disease Analysis)
An open source, standards compliant, high quality genomic epidemiology
analysis platform to support real-time (food-borne) disease outbreak
investigations
2 www.IRIDA.ca
3. 3
Each year, one in eight Canadians (or
four million people)
get sick with a domestically acquired
food-borne illness.
4. Partnership among public health agencies and academic institutes to bridge the gaps
between advancements in genomic epidemiology and application to real-life and real-
time use cases in public health agencies
- Project Team has direct access to state of the art research in academia
- Project Team is directly embedded in user organization
5. Interviews with key personnel to identify
barriers to implement genomic epidemiology in
public health agencies
5
6. GAP 1: PUBLIC HEALTH PERSONNEL
LACK TRAINING IN GENOMICS
7. Solution 1a: Build a User Friendly, high quality
analysis platform to process genomics data
• Carefully designed and engineered software platform is
just the starting point… User
Interface
Security
File system
Metadata
Storage
Application
logic
REST API
Workflow Execution Manager
Continuous Integration Documentation
8. • Easy to use interface hiding the technical details
Solution 1a: Build a User Friendly, high quality
analysis platform to process genomics data
9. Solution 1a: Build a User Friendly, high quality
analysis platform to process genomics data
10. Solution 1b: Build Portable and Transparent
Pipelines
• Use Galaxy as workflow engine – large
community support
• Retools to address usability, security, and
other limitations
• Version Controlled Pipeline Templates
• Input files, parameters, and workflow are
sent to IRIDA-specific Galaxy for execution
• Results and provenance information are
copied from Galaxy
1. Input
files sent to
Galaxy
3. Results
downloaded
from Galaxy
IRIDA UI/DB
Galaxy
Assembly Tools
Variant Calling Tools
…
REST API
Shared File System
Worker Worker
2. Tools executed
on Galaxy workers
11. Solution 1c: Start the training NOW!
• Canada’s National Microbiology Laboratory has hosted
genomic workshops for partners and collaborators
• IRIDA Project has dedicated funding for hosting workshops in
4Q of 2015 and 2016
• We would like to hear about other training initiatives and
share experience and training material
13. Many Players in surveillance and outbreak –
ineffective information sharing
Source: M. Taylor, BCCDC
Provincial public
health dept.
National laboratory
Local public
health dept.
Provincial
laboratory
Cases
Physicians Frontline lab
Information
BioinformaticsandAnalyticalCapacities
14. Many Systems used in Reporting Diseases –
require data re-entry and re-coding
National Ministry of
Health
Provincial public
health dept.
National laboratory
Local public
health dept.
Provincial
laboratory
Cases
Physicians Local laboratory
Fax/Electronic
Fax
Phone/Fax
Electronic/Paper
Electronic/Fax/Phone
Mailing of
Samples/Fax/Eelctroni
c
Source: M. Taylor, BCCDC
15. IRIDA is designed with these dilemma in mind
• Solutions:
– 2a: Localized Instance of federated databases
– 2b: Permission Control – authentication /authorization for
information sharing
– 2c: User role-based display of information
16. Solution 2a: Local/Cloud Instances and Data
Federation
• Data processing capacity pushed to data generating
labs
• Allow data sharing securely for enhanced analysis
• Eventually cultivating a culture of openness of data
sharing and collaborative development of tools
16
17. Authorization
Solution 2b: Security
• Local authorization per instance.
• Method-level authorization.
• Object-level authorization.
• Allow secure, fine grained and
flexible information sharing
18. Solution 2c: Role-based Dynamic Display driven
by Ontology
• Ontologies often lack a content management system (CMS)
• An Interface Model Ontology (IFM) can define a CMS for an
ontology
19. IFM Interface View Permissions
Detailed View Restricted View
E.g. User role permissions control visibility and editing of content
21. Solution 3a: Use Ontology
• Ontology: a way to describe types of entities
and relations between them
• Why use ontology
– Ontology is flexible and expandable
– Lower levels of expressivity (e.g. controlled vocabulary,
data dictionary) are heavy handed and show low level of
compliance and adoption
– Free text used as an alternative that are not computing
friendly
– Ontology and semantic web technologies may be a
solution
22. Many Domains of Knowledge are needed to describe
an outbreak investigation Build On, Work With:
OBI
TypON
NGSOnto
NIAID-GSC-BRC core metadata
MIxS Ontology
NCBI Biosample etc
TRANS – Pathogen Transmission
EPO
Exposure Ontology
Infectious Disease Ontology
CARD, ARO for AMR
USDA Nutrient DB
EFSA Comp. Food Consump. DB
Example gaps to be filled:
Expand food ontology; expand CARD
AMR data with others.
23. Lab Checklist/Ontology
• Currently finishing a lab/genomics checklist and
starting an epidemiology checklist
• Metadata Domains:
– Sample Collection
– Sample Source
– Environmental
– Lab Analytics
– Sequencing Process /QC
– Sequencing Run /QC
– Assembly Process / QC
– Others overlapping with Epi: Demographic / Geographic /
etc.
24. GAP 4: GENOMIC DATA
INTERPRETATION IS COMPLEX AND
TECHNOLOGY IS EVOLVING
25. Solution 4a: Use of QA/QC in IRIDA
• Software Engineering
– High quality software that meets regulatory guidelines
– Open Source product to ensure “white box” testing
– Ontology driven software development
– Follow proper software development cycle
• Data Quality
– Built-in modules to check for input data quality
– Warnings and Feedbacks during pipeline execution to laboratory technologists
– Use of Ontology to check metadata (non-genomic) data quality
• Analytic Tool Quality
– Utilize validation datasets
– Use of abstract pipeline description – with version control
– Periodic analysis of exceptions and boundary cases to assess tool accuracy
26. Solution 4b: Generation of validation datasets
To Participate, Contact
Rene Hendriksen
rshe@food.dtu.dk
Or
Errol Strain
Errol.Strain@fda.hhs.gov
http://www.globalmicrobialidentifier.org/Workgroups#work-group-4
27. Solution 4c: Exploratory tools can access certain
data via REST API securely
27
http://pathogenomics.sfu.ca/islandviewer
IslandViewer
Dhillon and Laird et al. 2015, Nucleic Acids
Research
http://kiwi.cs.dal.ca/GenGIS
Parks et al. 2013, PLoS One
28. Availability
• Jun 1 2015: IRIDA 1.0 beta Internal Release
– Release to collaborators for installation and full test
• Jul 1 2015: IRIDA 1.0 beta1
– Announce Beta release, download, documentation
available on website – www.irida.ca
• Aug 1 2015: IRIDA 1.0 beta2
– Cloud installer, with documentation
– Additional pipelines as available
– Visualization as available
29. Acknowledgements
Project Leaders
Fiona Brinkman – SFU
Will Hsiao – PHMRL
Gary Van Domselaar – NML
University of Lisbon
Joᾶo Carriҫo
National Microbiology Laboratory (NML)
Franklin Bristow
Aaron Petkau
Thomas Matthews
Josh Adam
Adam Olson
Tarah Lynch
Shaun Tyler
Philip Mabon
Philip Au
Celine Nadon
Matthew Stuart-Edwards
Morag Graham
Chrystal Berry
Lorelee Tschetter
Aleisha Reimer
Laboratory for Foodborne Zoonoses (LFZ)
Eduardo Taboada
Peter Kruczkiewicz
Chad Laing
Vic Gannon
Matthew Whiteside
Ross Duncan
Steven Mutschall
Simon Fraser University (SFU)
Melanie Courtot
Emma Griffiths
Geoff Winsor
Julie Shay
Matthew Laird
Bhav Dhillon
Raymond Lo
BC Public Health Microbiology &
Reference Laboratory (PHMRL) and BC
Centre for Disease Control (BCCDC)
Judy Isaac-Renton
Patrick Tang
Natalie Prystajecky
Jennifer Gardy
Damion Dooley
Linda Hoang
Kim MacDonald
Yin Chang
Eleni Galanis
Marsha Taylor
Cletus D’Souza
Ana Paccagnella
University of Maryland
Lynn Schriml
Canadian Food Inspection Agency (CFIA)
Burton Blais
Catherine Carrillo
Dominic Lambert
Dalhousie University
Rob Beiko
Alex Keddy
29
McMaster University
Andrew McArthur
Daim Sardar
European Nucleotide Archive
Guy Cochrane
Petra ten Hoopen
Clara Amid
European Food Safety Agency
Leibana Criado Ernesto
Vernazza Francesco
Rizzi Valentina
