CAP Feedback Session, CZI Seed Networks 2020

Transcript

1. Cell Annotation Platform Feedback Session Evan Biederstedt evan_biederstedt@hms.harvard.edu Peter Kharchenko Lab
 Harvard Medical School
2. • Introduction to Cell Annotation Platform (CAP) • Motivation • Architecture & Use Cases • Questions & Feedback After Presentation Contact: evan_biederstedt@hms.harvard.edu 2 Agenda
3. Motivation https://science.sciencemag.org/content/368/6490/497 Researchers manually examine prominent molecular patterns in light of prior biological knowledge, and annotate cells. Problem There’s no standard source of accumulated annotations with associated molecular data for researchers to explore
4. 4 Motivation NK Cells Cytokines Monocytes Problem • Individual research groups end up annotating (potentially millions of) cells manually, which results in cells with inconsistent terms and labelings between groups. • This approach cannot scale. • There's no medium for researchers to compare annotations across studies, potentially resolving con f l icting results/ nomenclatures. • No central location to access annotations used in publications.
5. Cell Annotation Platform (CAP) • Platform to create, explore, and store annotations • Allow users to compare annotations (with associated molecular pro f i les) within and across datasets • Provide a medium for researchers to converge upon a consensus nomenclature • Standardize collections of annotations, empowering researchers to reproduce analyses • Enable automated cell annotation methods
6. 6 Main Components Data Upload & Publish Interactive Annotation UI CellCards View Homepage •CAP Homepage •Data Upload & Publish •Interactive Annotation UI •“CellCards” View
7. Published Annotations Interactive UI “CellCards” View
8. View Annotations Interactive UI • View molecular data • Di f f erential expression analysis • Access embeddings “CellCards” View • CellName de f i nitions • Molecular signatures + marker genes • Related datasets
9. http://vitessce.io/ Annotate Datasets via Interactive UI Annotation • CellName: cell label de f i nitions • CellSets: cell labels mapped to cell IDs • Metadata: species, protocol, organ, tissue Annotation
10. Upload Annotations Annotation • CellName: cell label de f i nitions • CellSets: cell labels mapped to cell IDs • Metadata: species, protocol, organ, tissue Parsing User Prompt Type of Files
 •AnnData •Seurat •Loom • CAP f i le format Project • Collection of Annotations associated with a username • Access for collaborators • Ability to edit, view annotations Upload Methods
 •GUI •CLI (ftp for bulk uploads) •git tracking
11. Upload Annotations Annotation • CellName: cell label de f i nitions • CellSets: cell labels mapped to cell IDs • Metadata: species, protocol, organ, tissue User Prompt Type of Files
 •AnnData •Seurat •Loom • CAP f i le format Git Tracking Command Line Interface (CLI) Options
12. Upload Annotations Annotation • CellName: cell label de f i nitions • CellSets: cell labels mapped to cell IDs • Metadata: species, protocol, organ, tissue Parsing User Prompt Type of Files
 •AnnData •Seurat •Loom • CAP f i le format Error Handling Upload Methods
 •GUI •CLI (ftp for bulk uploads) •git tracking
13. Publish Annotations Version • Published Annotation for manuscripts Check Project •Collections of Annotations •Access restricted to collaborators
14. Publish Annotations Check Error Handling Project •Collections of Annotations •Access restricted to collaborators
15. Feedback? Questions? Feedback Session Please send further feedback to: evan_biederstedt@hms.harvard.edu Acknowledgements: Peter Kharchenko Lab Colin Maher Nick Akhmetov PK https://github.com/kharchenkolab