The Goal of IRIDA
We are developing a free, open source, interactive, standards compliant web platform to support real-time infectious disease outbreak investigations using genomic data. The IRIDA platform, freely available from our download page, aims at public health agencies
Currently, IRIDA offers:
- Management of strain and genomic sequence data
- Rapid processing and analysis of genomic data
- Informative display of genomic analysis results (genome annotation and phylogenetic relationships)
- Federated access of data via standardized REST API
- Open source (under Apache 2.0 license)
Additional functionalities currently being implemented:
- Dynamic integration of data sources (clinical, epidemiological and lab sourced)
- Privacy protection
- Integration of additional bioinformatics tools for researchers and public health workers
- Data standardization enabling value-added activities
IRIDA’s Design Philosophy
The IRIDA (Integrated Rapid Infectious Disease Analysis) platform will provide programs and platforms for users across Canada and around the world to manage outbreaks and perform microbial surveillance activities. IRIDA software and Illumina MiSeq instrumentation, scheduled to be rolled out to Provincial Reference labs by the National Microbiology Laboratory in 2016, will be accompanied by IRIDA training packages to allow public health users to understand the clustering of isolates and to produce the nomenclature required to identify outbreaks and differentiate sporadic cases. The IRIDA platform is being designed in consultation with local, provincial national and international stakeholders to ensure usability and improve interoperability with current systems and programs. Consultation by the design team with end users is critical to ensure that all the required and desired functionalities are implemented, that we capture all the patient and sample information available, and that these elements have the highest accuracy and efficiency achievable.
The benefits of IRIDA include:
- Control over data: labs and health authorities maintain ownership and control over their data through federated access. You can use the built-in ontology to track in-house turn around times, investigation trends, baselines of incidence etc which will only be seen by you and your organization. Agencies can customize the labels of data fields to fit the systems they already use, while IRIDA’s backend ontology integration will coordinate these labels for interagency comparisons. Reporting/exporting of data is facilitated by customizing the fields you want to share. In this way, IP rights are maintained during sharing as you control what metadata other groups are allowed to see e.g. customization of line lists can be achieved simply through stakeholder permissions rather than reformatting of files.
- More efficient and accurate data entry: IRIDA is working towards mechanisms for extracting/exporting data from existing programs and reporting systems such as CNPHI, LIMS and Bionumerics which will facilitate automated entry across platforms. Standardized vocabulary will reduce spelling mistakes and typos and allow for report generation and trend tracking.
- Improved typing results: IRIDA provides user-friendly pipelines that are customizable by your in-house bioinformatics experts for specialized applications. Thresholds for including isolates in clusters as well as criteria for interpretation, as determined by genomic epidemiology experts around the world, will be validated, accredited and monitored by PulseNet-Canada. In this way, information and data quality will be improved by better, standardized data entry as well as visualization features for users and stakeholders.
By enabling the sharing of WGS data between lab analysts, epidemiologists, stakeholders and academics, data within IRIDA can be leveraged for improved patient health, faster trace back for contamination control as well as discovery and expert analysis of genetic events and phenomena which impact health outcomes.