HCA Asia 2023, November 27, CAP talk

https://events.humancellatlas.org/2023Asia/agenda

Transcript

1. Evan Biederstedt De fi ning Cell Types and States for the Human Cell Atlas and Beyond 1 Cell Annotation Platform
2. Outline: 10 minute talk 2 1. Motivation: Problem & Why CAP? 2. *Quick* CAP overview 3. Start thinking about Cell Annotation Jamborees
3. Problem: Why do CAP? 3 Problem #1: Community standards & reproducibility Problem #2: Solution for creating human cell atlases
4. https://www.nature.com/articles/s41588-021-00818-x MKI67: gene associated with cellular proliferation HBB: gene associated with hemoglobin production PAX2: gene associated with kidney development Motivation: Cell Annotations 4
5. Problem #1: Community Standards https://www.nature.com/articles/s41588-021-00818-x 5 How? How were these cell annotations created? What? What do the “labels” mean? Who? When?
6. Problem #1: Community Standards 6 https://www.science.org/doi/10.1126/science.aay0267 How? How were these cell annotations created? What? What do the “labels” mean? Who? When?
7. Problem #1: Community Standards https://www.nature.com/articles/s41588-021-00818-x 7 Scientific Reproducibility Transparency Scientific Communication Trust or distrust these cell annotations?
8. Problem #2: Creating Human Cell Atlases 8 (related to the first problem)
9. Inconsistent terms 9 • Free text • Abbreviations https://www.nature.com/articles/s41588-021-00818-x https://www.science.org/doi/10.1126/science.aay0267
10. Di ff erent granularity 10 • “Precise” vs “broad” annotations https://www.nature.com/articles/s41588-021-00818-x https://www.science.org/doi/10.1126/science.aay0267
11. 11 Researchers have opinions Cell annotations di ff er between researchers • Di ff er in terms of de fi nitions of cell types/cell states • Di ff er in terms of terminology/vocabulary used • Di ff er in terms of precision of terminology/vocabulary • Di ff er in terms of molecular signatures
12. Cell Annotation Metadata Requirements • Name of set of annotations • Free-text cell type term • Full name • Exists in Cell Ontology (CL)? • Closest CL term • Rationale/explanation for cell annotation • Marker genes used to de fi ne cell term • Canonical marker genes • Synonyms, categories for cell type entity • (Optional) other “biological markers” used • Manual annotation or algorithmic annotation or both? • Necessary context required to work with cell annotations
 • HCA researchers MUST provide these
 • All fi elds provided by researchers; checked by data curators Solution: Community Standards
13. Main Components • Data Repository • Private Collaborative Workspaces • Annotation UI: Browse & Create Annotations • “CellCards” Reference Summaries • Cell Annotation Platform (CAP)
14. • Collections of datasets, typically corresponding to a scienti fi c journal article • Timestamped
 • DOIs for citations in journals
 • Versioning • Downloaded annotations in standardized formats 
 Publications 14
15. User roles: • viewer (read-only) • editor (write access) • owner (administrative) • 
 • User Roles 15 Keep your data private until ready!
 
 Save until ready for public, and then publish
16. UI: Interactive Exploration & Annotation Contact us for UI Interviews
17. Crowdsourcing Consensus Text-based Molecular-based
18. 18 HCA = “community-driven” Consensus: Cell Annotation Jamborees
19. 19 Cell Annotation Jamborees Consensus • Address disagreements • Several rounds of votes • Majority vote = atlas?
20. Thank you! •Fabian Theis •Nils Gehlenborg •David Osumi-Sutherland •Aviv Regev •John Marioni •Peter Kharchenko •Chloé Villani 20
21. Special thank you! • Can Ergen-Behr • Nir Yosef • Felix Fischer • Ellen Todres • Lucia Robson • HCA Sta ff & many others! 21
22. Maxim Svetlakov Maxim Sokolov Andrey Isaev Michael Loktionov Denis Ilguzin Mary Futey Nick Akhmetov Lusine Barseghyan Kirill Goryakin Konstantin Boyandin Uğur Bayindir Levon Ghukasyan Artyom Miskaryan Pavel Istomin Denis Bolgov Roman Mukhin Evan Biederstedt