The Human Cell Atlas Data Coordination Platform
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The Human Cell Atlas aims to create a comprehensive reference map of all human cell types and their properties, serving as a foundation for understanding health and disease. The Data Coordination Platform (DCP) facilitates the organization and accessibility of large data sets generated by multiple labs worldwide, ensuring that data is open and standardized. Future goals include further development of community-driven metadata standards and enhancing data accessibility for researchers through various tools and interfaces.
The Human Cell Atlas Data Coordination Platform
- 1. The Human Cell Atlas Data Coordination Platform March 20th 12th CeBiTec Symposium Big Data in Medicine and Biotechnology Center for Interdisciplinary Research (ZiF), Bielefeld University Laura Clarke
- 3. A “google maps” of human anatomy
- 4. Goal : A periodic table of our cells
- 5. To create a comprehensive reference map of the types and properties of all human cells, the fundamental unit of life, as a basis for understanding, diagnosing, monitoring, and treating health and disease Human Cell Atlas: Mission
- 6. Experimental Approach The Art of Clean Up, Ursus Wehrli, Kimberly Vardeman
- 7. Experimental Approach The Art of Clean Up, Ursus Wehrli, Kimberly Vardeman Bulk population based methods
- 8. Experimental Approach The Art of Clean Up, Ursus Wehrli, Kimberly Vardeman Bulk population based methods Single Cell Methods
- 9. Experimental Approach The Art of Clean Up, Ursus Wehrli, Kimberly Vardeman Bulk population based methods Single Cell Methods Spatial methods
- 10. Phase I status update
- 11. Ensure the data is open and accessible to all researchers Encourage innovation on computation methods Enable sharing of new methods and technologies Organize and standardize terabytes of data for billions of cells, across multiple modalities, generated by hundreds of labs around the world. Data Coordination Challenges
- 12. The Data Coordination Platform
- 13. The Team 62 scientists and engineers 4 different locations 3 time zones ~30 video conferences a month
- 14. How far the DCP has come
- 15. The Data Coordination Platform Cloud-based Open Modular International
- 16. Data Generators Many submitters Global community Diversity of biology Specialists / cores
- 18. Store Writes valid data and metadata Unique versioned identifiers Cloud replication
- 19. Open Data Raw data immediately available Notification system with events
- 20. Analysis Pipelines Standardized analysis pipelines Analysis Working Group Full transcript scRNA-Seq 3’ scRNA-seq Portability
- 21. Standardized Results Analysis products written using Ingest Products are stored in the data store
- 22. Data Access Search, download, and compute on all data Web Browser Command Line Multiple Clouds
- 23. What is next for the DCP?
- 24. The Data Coordination Platform and the Community Data Commons
- 25. HCA metadata standards are: Agile Modular Flexible Validated Open Community driven Ensuring HCA data is FAIR https://github.com/HumanCellAtlas/metadata-schema
- 26. Simple entities and flexible relationships
- 28. Tertiary portals
- 29. ● Save searches as collections ● Share search collections ● Download files (FASTQ, bam, tiff, expression matrix, etc) Browsing the data https://www.flaticon.com
- 30. ● Filter for a set of data in the Data Browser ● “Handoff” mechanism to Tertiary Portals for analysis/visualization ● Sends search results Hand data to the tertiary portals Launch https://www.flaticon.com
- 31. ● What do you need from the DCP? ○ Submission ○ Discovery ○ Analysis Join Slack http://join-slack.humancellatlas.org/ See our code https://github.com/humancellatlas Email data-help@humancellatlas.org How to get involved?
- 32. HCA registered members: 44 countries, 341 institutes
- 33. Thanks! Mallory Freeberg Vladimir Kiselev Irene Papatheodrou Brian O’Conor Aviv Regev Sarah Teichmann Timothy Tickle Mike Stubbington