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obophenotype / provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL
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Compare metadata single cell datasets from multiple platforms #42

Open shawntanzk opened 1 year ago

shawntanzk commented 1 year ago

Coordinated here: https://docs.google.com/spreadsheets/d/1MAWl4exteFSpCyIlpE8tzqfc-rCsu3cncllNSLn5o-0/edit?usp=sharing

Hi Shawn and Bradley - following on from today’s discussion, I’d really like to be able to do a side by side comparison of metadata on the same single cell datasets from multiple platforms: HCA data portal https://data.humancellatlas.org/explore/projects/ celltype.info https://cellxgene.cziscience.com/collections Azimuth (although still not very much on there) Allen Brain Atlas (can we download matrices directly from there) / Nemo Problem - finding candidate sets to compare. We should have one brain and one-non-brain. Non-brain should be something with some detailed annotation. Brain - should probably be mini-atlas. Challenge might be dataset size. Non-brain. Kidney might be good, although struggling to find example (CAP needs to show publication!) What to compare: Keys used for standard metadata How ontologies are supported How cell type is recorded - what, if anything is lost in flattening Relationship metadata content to display on site.