Transfer from CL: Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

obophenotype / provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL

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Transfer from CL: Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes #36

Open shawntanzk opened 2 years ago

shawntanzk commented 2 years ago

From https://github.com/obophenotype/cell-ontology/issues/519

"https://www.nature.com/articles/s41467-018-05134-3

40 proposed RGC subtypes

Unclear how these would be represented but making a ticket anyway"

shawntanzk commented 2 years ago

Questions:

is this hosted anywhere? (eg CellXgene, or projection platform etc.)
what is the minimal job we can do to get things in (we don't need details)

@addiehl - was there work done on retinal ganglion cells work done on your side before? we might be able to incorporate this (however its low priority for us given resources)

addiehl commented 2 years ago

Hi Shawn, You might want to look at the attached RCL-merged.owl.zip file, which includes work by Patrick Ray and Terry Meehan from 2011 (@patrick-lloyd-ray), sadly never incorporated into CL. I think the cell types you are interested in are all in the CL:0004000 range.

Note that 23 of these cell types are cross reference with BAMS. Since none of these CL IDs have ever been used, you can move them into the current ontology file if you wish.

Alex

patrick-lloyd-ray commented 2 years ago

Thanks, @addiehl.

If you decide to use some of that work, I can help as needed, @shawntanzk.