Infectious diseases continue to exact a substantial toll on health and health-care resources – accounting for nearly a quarter of the estimated 52.8 million deaths annually, as well as hundreds of billions of dollars in lost productivity representing a significant percentage of global GDP. Microbial organisms, however, are also critical for healthy ecosystems, are sources of bioactive compounds and metabolic energy, and have a wealth of other beneficial properties.
Whole genome sequencing (WGS) is a powerful tool for understanding the evolution, prevalence and distribution of microbes in hosts and environments around the world owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods.
The Global Microbial Identifier (GMI) envisions a global, real-time system for microbial DNA data and minimal metadata exchange and analysis for public health, food safety, agricultural, animal and environmental surveillance, investigations, as well as research and innovation. In September 2011, the first meeting was held in Brussels with the aim of developing a common platform and to better understand the potentials of an interactive microbiological genomic database. Since that initial meeting, GMI has held 11 international conferences in 9 countries across 3 continents. GMI has been a leader in the microbial genomics community, with a number of successes such as the development of MDM (the minimal metadata required for matching isolates), the creation of benchmark datasets for pipeline validation and tool comparisons for increase reproducibility in bioinformatics analyses, and establishing proficiency tests for quality assurance of NGS assays in laboratory settings. GMI accomplishes its goals and objectives through the efforts of four working groups; WG1 – Policy and networks, WG2 – Metadata standards and repositories, WG3 – Pipelines and analytical approaches, WG4 – Proficiency testing and ring trials.
In 2020, GMI will be held in Canada for the first time ever. GMI13 will continue this legacy by focusing on the critical importance of equity and interoperability (semantic, process, systems) in developing a global microbial genomics data sharing ecosystem. The goals of GMI13 are summarized in the GMI13 Vision Statement.
Vision Statement – GMI13
The Global Microbial Identifier (GMI) envisions a global, real-time system for matching microbial strains through the sharing of microbial genomic data and minimal metadata to facilitate infectious disease surveillance, food safety regulation, biodiversity monitoring, outbreak investigations, as well as research and innovation. Critical to achieving that goal is the ability of different organizations to share sequence and contextual data quickly with each other and with a centralized repository (i.e. INSDC). Given the sensitivity of certain types of contextual data, the array of technologies available, variable national policies and diverse organizational mandates involved in genomics data sharing, GMI must work towards building an ecosystem of different interconnected working parts – with an emphasis on open source software and workflows, reproducible analyses, data standards, accessible/deployable laboratory assays and portable bioinformatics applications. Partners in the ecosystem must have agency to participate in the way that they choose, and GMI must work with partners to build trust and capacity in sequencing, bioinformatics and data sharing.
GMI13 will focus on reassessing strategies and milestones for realizing a data sharing ecosystem. Themes will include i) technical mechanisms and data standards for enabling interoperability, reproducibility, and comparability of results; and ii) frameworks for building trust and equitable benefit sharing.
- Explore the “genomics-based data sharing ecosystem”
- Assess data standards for better data harmonization and sharing between public and private repositories
- Understand challenges and possible solutions for equitable data sharing
- Establish connections with existing genomics-based networks (e.g. GA4GH, PHA4GE, International Organization for Standards (ISO))
- Reassess work groups to improve continuity or participation and efficacy of function