Write runner script to convert scxa files to cxg h5ad and rdf

EBISPOT / scxa_2_cxg

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Write runner script to convert scxa files to cxg h5ad and rdf #12

Closed dosumis closed 1 month ago

dosumis commented 5 months ago

[x] runs conversion all scxa files to cxg h5ad
[x] runs Pandasaurus on all files to generate rdf to load into OBASK
[x] runs robot template pipeline to glue content together.

anitacaron commented 3 months ago

runs Pandasaurus on all files to generate rdf to load into OBASK

Could you please be more specific about this item? :)

dosumis commented 3 months ago

@ubyndr has written a pipeline to run this for our KG. We should be able to re-use this pipeline with relatively minimal adaption.

@ubyndr - I haven't had a chance to look yet. I'm assuming makefile + robot with curated tables as input => resolution to CxG files.
For SCXA Curation for CxG = curation of author cell type label fields. Not sure we need that for SCXA.

ubyndr commented 3 months ago

I have shared the scripts I wrote with Anita and explained what she needs to do.

anitacaron commented 3 months ago

It would be good to discuss about the author cell type label in the meeting today.

anitacaron commented 1 month ago

All done in the two linked PRs.