1. MongoDB and the Connectivity Mapmaking connections between genetics and disease

2. . 3. . 4. . 5. . 6. .Coreycflynn@broadinstitute.org@CoreyJFlynn 7. Gene Expressiona common language for biology 8. . 9. . 10. . 11. . 12. . 13. .132006~7,000 experimentsOver 19,000 registered usersCited by over 1,200 scientific reports 14. .2006 15. .2014 16. .16 17. Connectivity Map Dataset1.4 million gene expression profiles12,488 Compounds FDA approved drugs Bioactive tool compounds Screening hits3,800 Genes (shRNA & cDNA) Targets/pathways of approved drugs Candidate disease genes Community nominations15 Cell types Banked primary cell types Cancer cell lines Primary hTERT-immortalized Patient-derived iPS cells Community nominated 18. Connectivity Map DataEasy to describe, tough to Model Diverse users and use-cases Annotations are complex and oftenincomplete Frequent updates 19. Data ModelAn agile philosophy keeps the model tractableStore just whats neededTest and use dailyRefactor frequently 20. Data ModelAn agile philosophy keeps the model tractableStore just whats neededTest and use dailyRefactor frequently 21. Data ModelAn inventory of signaturessignature_info 22. Data ModelShared fields as separate collectionssignature_infocell_info 23. Data ModelShared fields as separate collectionssignature_info treatment_info 24. Data ModelAdd computed fields and external meta-datasignature_info cell_info 25. Data ModelDenormalize to optimize lookupssignature_info treatment_info 26. APIsAre awesome, life science needs more of them/siginfo/cell/A 27. APIsAre awesome, life science needs more of them/siginfo?q={cell:A} 28. APIMongoDB inspired a rich query syntaxFunction ExampleQuery /siginfo?q={cell:A,name:B}Field selection /siginfo?q={}&f={name:1}Document count /siginfo?q={}&c=trueDocument limit /siginfo?q={}&l=10Skip documents /siginfo?q={}&l=10&sk=10Sort order /siginfo?q={}&s={name:-1,cell:1}Distinct values /siginfo?q={}&d=nameAggregation /siginfo?q={}&g=name 29. APINode and Mongoose enable easy API creation 30. Language BindingsJSON as a universal formatJavascriptPythonR 31. Analytic ToolsA compute API liberates command line scripts 32. Compute APIMessage queuing via a capped collection 33. A research platform for functionalgenomics 34. Predicting Drug FunctionDiverse structures, common activities 35. Predicting Drug FunctionDiverse structures, common activitiesVEGFR inhibitorPPARG agonistPI3K/MTOR inhibitorROCK inhibitorEstrogen agonist 36. Finding Novel Drug TargetsRepurposing failed drugsOriginal target 37. Finding Novel Drug TargetsRepurposing failed drugsOriginal targetFailed in Phase 2 clinical trial due to lack of efficacy 38. Finding Novel Drug TargetsRepurposing failed drugsOriginal targetNovel Target ANovel Target BNovel Target CNovel Target D