Building a Global Search Engine for Genetic Data
- 1. #DevTO @mirocupak Miro Cupak VP Engineering, DNAstack 30/04/2018 Building a global search engine for genetic data
- 2. #DevTO @mirocupak What and why? !2 ⢠Beacon Network (https://beacon-network.org/) ⢠Beacon Project from the Global Alliance for Genomics and Health (GA4GH) ⢠largest search and discovery engine of human genomic variation
- 3. #DevTO @mirocupak Beacon !3 ⢠experiment to test the willingness of international sites to share genetic data in the simplest of all technical contexts ⢠design principles ⢠A beacon has to be technically simple. ⢠A beacon has to minimize risks associated with genomic data sharing. ⢠It has to be possible to make a beacon publicly available. ⢠simple web service allowing users to query institutionâs databases to determine whether they contain a genetic variant of interest ⢠started in March 2014, quickly gained traction ⢠receives questions of the form Do you have information about this mutation? ⢠responds with yes or no, optionally with additional information about the mutation
- 7. #DevTO @mirocupak Standard !7 ⢠0.1 (2014): simple, Apache Avro ⢠0.2 (2015): complex, datasets, self description, Apache Avro ⢠0.3 (2016): simpliďŹed, improved, modular and extensible, tooling, moving towards Protocol Buffers ⢠0.4 (2018): ďŹexible, complex variants, data use conditions, developer- friendly, OpenAPI ⢠now working on 0.4.1, 0.5 coming soon, 1.0 in 2018
- 8. #DevTO @mirocupak Beacon Network !8 ⢠federation of queries across beacons ⢠de-facto registry ⢠programmatically accessible, uniďŹed beacon API ⢠aggregation ⢠participant resolution ⢠ďŹexible, dynamic and easily extensible query execution pipeline - query parameter translation, request construction, response fetching over network, parsing
- 10. #DevTO @mirocupak Size !10 ⢠~100 installations, 40 institutions, 18 countries, 6 continents
- 11. #DevTO @mirocupak Users !11 ⢠13k users, 136 countries
- 13. #DevTO @mirocupak !13 Other fun stats ⢠popular parameter values ⢠variants ⢠deleteriousness ⢠rarity ⢠genes ⢠disorders and clinical abnormalities