GenomeTrakr: Perspectives on linking internationally - Canada and IRIDA.ca

1. 1 Perspec)ves on Linking Interna)onally – Canada and IRIDA.ca Fiona Brinkman Professor, Department of Biochemistry and Molecular Biology Adjunct, School of Compu>ng Science, and Faculty of Health Sciences Simon Fraser University Greater Vancouver, BC, Canada brinkman@sfu.ca GenomeTrakr -‐ Sept 23 2015 @ﬁonabrinkman Canada’s Integrated Rapid Infec>ous Disease Analysis PlaTorm for Genomic Epidemiology

2. Interac(ng with, complemen(ng others Interna(onal resources Integrated Rapid Infec4ous Disease Analysis informa4cs pla;orm suppor)ng real-‐)me infec)ous disease outbreak inves)ga)ons Goal Rich genomic epi analysis Public health agencies Rapid, open genomic data release Academia/Public

3. Genomics, Epidemiology, Clinical, Lab Data Integrated Rapid Infec4ous Disease Analysis informa4cs pla;orm suppor)ng real-‐)me infec)ous disease outbreak inves)ga)ons Goal

4. User-‐friendly, web-‐accessible User access control (e.g. public health workers vs public) Automated assembly pipelines, Data analysis and visualiza(on Standards compliant, rich ontologies Open source Integrated Rapid Infec4ous Disease Analysis informa4cs pla;orm suppor)ng real-‐)me infec)ous disease outbreak inves)ga)ons Goal

5. National Public Health Agency Provincial Public Health Agency Academic/Public Will Hsiao Fiona Brinkman Gary Van Domselaar www.IRIDA.ca

6. 6 Project Leaders Fiona Brinkman – SFU Will Hsiao – PHMRL Gary Van Domselaar – NML Simon Fraser University (SFU) Emma Griffiths Geoff Winsor Julie Shay Matthew Laird Bhav Dhillon McMaster University Andrew McArthur Daim Sardar European Food Safety Agency Leibana Criado Ernesto Vernazza Francesco Rizzi Valentina IRIDA-mail@sfu.ca National Microbiology Laboratory (NML) Franklin Bristow Aaron Petkau Thomas Matthews Josh Adam Adam Olsen Tara Lynch Shaun Tyler Philip Mabon Philip Au Celine Nadon Matthew Stuart-Edwards Morag Graham Chrystal Berry Lorelee Tschetter Eduardo Toboada Peter Kruczkiewicz Chad Laing Vic Gannon Matthew Whiteside Ross Duncan Steven Mutschall University of Lisbon Joᾶo Carriҫo European Bioinformatics Institute Melanie Courtot Helen Parkinson BC Public Health Microbiology & Reference Laboratory (PHMRL) and BC Centre for Disease Control (BCCDC) Judy Isaac-Renton Patrick Tang Natalie Prystajecky Jennifer Gardy Linda Hoang Kim MacDonald Yin Chang Eleni Galanis Marsha Taylor Damion Dooley Jennifer Law University of Maryland Lynn Schriml Canadian Food Inspection Agency (CFIA) Adam Koziol Burton Blais Catherine Carrillo Dalhousie University Rob Beiko Alex Keddy

7. IRIDA Design: Carefully designed and engineered soHware plaIorm is just the star)ng point… User Interface Security File system Metadata Storage Applica)on logic REST API Workﬂow Execu)on Manager Con)nuous Integra)on Documenta)on Federated database model

8. Addressing ontology gaps Build On, Work With: OBI TypON NGSOnto NIAID-‐GSC-‐BRC core metadata MIxS Ontology NCBI Biosample etc TRANS – Pathogen Transmission EPO Exposure Ontology Infec)ous Disease Ontology CARD, ARO for AMR USDA Nutrient DB EFSA Comp. Food Consump. DB Example gaps to ﬁll: Improve Food ontologies, AMR data Ontology: Describes types of en((es and rela(ons between them

9. Analy)cal Tool Quality Control Module Quality Metrics Quality Control IRIDA’S QA/QC Model

10. IRIDA Workflows: Portable and Transparent Pipelines Use Galaxy as workflow engine Version Controlled Pipeline Templates 1. Input files, parameters 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. Example data analysis, visualiza)on tools IslandViewer/GenomeD3Plot – more ﬂexible GI/VF/AMR visualiza)on Dhillon BK et al 2015 Nucl Acids Res PMID: 25916842 Laird MR et al 2015 Bioinforma(cs PMID: 26093150 www.pathogenomics.sfu.ca/islandviewer/ github.com/brinkmanlab/GenomeD3Plot/

12. “SNVPhyl” SNV analysis Integra)ng genomics, geographic data (led by NML, Rob Beiko, Dalhousie U) http://kiwi.cs.dal.ca/GenGIS SNVPhyl Software Demo by Aaron Petkau and IRIDA poster by Emma Griffiths at #ASMNGS meeting Example data analysis, visualization tools

13. Challenges … for IRIDA … for interna)onal linkages 13

14. Challenges … for IRIDA … for interna)onal linkages Biggest challenge is NOT bioinforma(cs/soPware development 14

15. Challenges … for IRIDA … for interna)onal linkages Biggest challenge is NOT bioinforma(cs/soPware development It’s sharing 15

16. Canada’s Public Health System Challenges Provincial public health dept. National laboratory Local public health dept. Provincial laboratory Cases Physicians Frontline lab Informa)on Bioinforma)cs and Analy)cal Capaci)es Info lost as aggregate data from Frontline lab to national PH labs

17. $ Disease Reporting Informa)on Sharing is Highly Complex •  Variety of agreements, legisla)on •  Lack of standards (metadata, legal requirements) •  Fears of data release during ongoing inves)ga)ons, and IP concerns make provinces “risk averse”

18. Impact •  Impacts data sharing na)onally, interna)onally •  Also: Lack of rich example data impacts ontology, data standards development (ability for computers to share) Must communicate to countries: Get data sharing arranged early – both na(onally and interna(onally 18

19. Interna)onal data sharing -‐  Get data sharing arranged early -‐  Ensure alloca(on of adequate resources to set it up -‐  Share bioinforma(cs resources, code, parameters -‐  Share data examples -‐  Start simple: Agree on minimal genome metadata for rapid release 19

20. Interna)onal data sharing Pt. 2 -‐ Develop harmonized metadata for further data release -‐ Interoperable systems -‐ Current and well-‐maintained repositories -‐ Valida4on datasets for pipeline calibra)on -‐ User access control Open access à Opens opportuni)es, discoveries 20

21. A new hope… MLISA (Multilateral Information Sharing Agreement) •  Canadian multi-jurisdictional legal agreement •  Establishes standards re sharing, usage, disclosure and protection of PH info for infectious diseases and PH events •  Technical annexes (for example for WGS) can be developed to clarify specifically data to be exchanged PulseNet as a model for sharing (in part)

22. Can USA–Canada sharing be developed as a model? Flight paths across North America. Outbreaks follow flight paths more closely than simple geographic distance.

23. 23 IRIDA’s Role in International Data Sharing 1.  Application ontology for genomic epidemiology 2.  Metadata standardization 3.  Interoperability 4.  Sensitive field sharing secured via authorization 5.  Privacy protection and data security 6.  Compatible with International Health Regulations (2005) 7.  Aims to support federated design, plus open data sharing

24. 24 Sharing – via computers, people Its all about communica(on Computers – ontologies, data standards are key Humans – gemng them together is key…

25. 25 Sharing – via computers, people Its all about communica(on Computers – ontologies, data standards are key Humans – gemng them together is key…

26. Brinkman Lab Kayaking Trip Addi)onal key trainee funding and compu)ng infrastructure: We’re hiring!

GenomeTrakr: Perspectives on linking internationally - Canada and IRIDA.ca

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GenomeTrakr: Perspectives on linking internationally - Canada and IRIDA.ca