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A Federated Platform Enabling Richer Genomic Epidemiology Analysis in a Public Health Environment.
Franklin Bristow2, Josh Adam2, João André Carriço5, Mélanie Courtot 3,1, 10, Bhavjinder Dhillon1, Damion Dooley3, Emma Griffiths1, Judy Isaac-Renton3, Alex Keddy8, Peter Kruczkiewicz7, Matthew Laird1, Andrew MacArthur11, Thomas Matthews2, Aaron Petkau2, Lynn Schriml6, Julie Shay1, Eduardo Taboada7, Patrick Tang2, Joel Thiessen2,9, Geoff Winsor1, Robert G. Beiko8, Morag Graham2,9, Gary Van Domselaar2,9, William Hsiao3,4,The IRIDA Consortium and Fiona Brinkman1. www.irida.ca1Simon Fraser University, Burnaby, BC, Canada;2National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; 3BC Public Health Microbiology and Reference Laboratory, Vancouver, BC, Canada; 4University of British Columbia, Vancouver, BC, Canada; 5Faculty of Medicine, University of Lisbon, Lisbon, Portugal; 6University of Maryland School of Medicine, Baltimore, MD, USA; 7National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada; 8Faculty of Computer Science, Dalhousie University, Halifax,NS, Canada; 9University of Manitoba, Winnipeg, MB, Canada, 10European Bioinformatics Institute, Hinxton, Cambridge, UK, 11McMaster University, Hamilton, ON, Canada.
The Goal of IRIDA:To support real-time infectious disease outbreak investigations in Canada:
We are developing an open source, interactive, standards compliant resource for public health agencies that aims to release de-identified genome data rapidly, plus enable rich epi-clinical-lab-genome data analysisin a Public Health environment.
Design Philosophy• Dynamic integration of data sources (clinical,
epidemiological and lab sourced) • Privacy protection • Suite of bioinformatics tools for researchers and
public health workers • Data standardization enabling value-added activities
Data Management and Analysis• Easy-to-use tools providing rich analyses in a timely
manner • Controlled parameters and workflows for reproducibility
• Automated raw read uploader• Data organized by Project and Sample• SNV phylogenies with SNVPhyl Galaxy workflow and de
novo assembly and annotation using SPAdes and Prokka• Easy-to-interpret QA/QC, revision tracking
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Data Security and Sharing • Stakeholders maintain local, physical ownership of
sample data • Data sharing facilitated over an HTTP REST API,
authorization with OAuth2
Application Ontology and User Interface• No single existing ontology can adequately describe all the
domains required for genomic epidemiology
• IRIDA ontology leverages existing resources and OBO standards for interoperability
• Metadata gaps identified by extensive user consultation IRIDA ontology available as OWL file
• Dynamic ontology driven user interface, selective de-identification and line list sharing
Identifies genomic islands (GIs), virulence factors, antibiotic resistance genes in complete and draft genomes
Integrates sequence data and geospatial information for phylogeographicanalysis
AMR gene annotation tool for whole genomes or genome assemblies integrated within Comprehensive Antibiotic Resistance Database (CARD)
Background• Most tools/pipelines require considerable technical
knowledge • Cannot easily integrate rich epidemiologic data
IslandViewer
GenGIS
RGI – Resistance Gene IdentifierDatabase & API Modules
User access control + Data Security
Quality
Control
Comparative
Genomics
Molecular
Typing
VisualizationPatho-
genomics
Genomic
Epi/Geo-
tagging
Lab Technician/
Medical
Microbiologist
Epidemiologist Researcher
Customized output
Clinical Data
Sources
Epidemiology
Data
Sources
Laboratory
Data
Sources
Programming Interface, Analysis
Modules, End Users
Data Sources
Value Added
Activities
Epidemiology Investigation
Results
Epi-analysis Ready Data
Outbreak Investigation
IRIDA Platform Design
AcknowledgementsFunded by grants from Genome Canada, Genome BC, the Genomics R&D Initiative (GRDI), Cystic Fibrosis Canada and Compute Canada
Genomics
Pathogen Taxonomy
SOPS
Diagnostic Test
Result Report
Laboratory-test centric
Clinical-patient centric
Epidemiology-case centric
Host Taxonomy
Symptoms
Demographics
Treatment
Vaccines
DrugsGeography
Public Health Intervention
Exposure
Contact
Food
Travel
Environment
Temporal Info
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