Publish - Siletti whole brain datset in CAS

[dosumis]

Status: Draft

This is an EPIC intended for grouping tasks. Component tasks should have single assignees on their own tickets.

Publication of Siletti whole brain datset in CAS is needed to BICAN and will serve as a public showcase of a dataset annotated using with CAS (BICAN extension). Publication should be as CAS and AnnData following both expanded and minimal conversions.

Dependencies:

Current curation in spreadsheets needs to be finalised (approval from authors pending) @mfutey & @dosumis to finalise. and standardised - see cellannotation/cell-annotation-schema#25 Scripts/pipelines need to be in place to convert spreadsheets to CAS. @ubyndr Scripts needed to pull barcode lists from anndata files - e.g. see https://github.com/cellannotation/cell_bx_extractor/blob/main/bx_extractor_script.py and to generate BICAN-compliant checksum-based cell-set accessions. @hkir-dev / @ubyndr AnnData conversion scripts need to be written, released and tested. @ubyndr cellannotation/cas-tools#7 cellannotation/cell-annotation-schema#42

[dosumis]

@hkir-dev As this is now working to the point where we have a high quality draft conversion. Can this be moved to it's own repo with a PURL release.? Two files: non-neuronal and neurons.

[hkir-dev]

Repos:

• https://github.com/brain-bican/human-brain-cell-atlas_v1_neurons
• https://github.com/brain-bican/human-brain-cell-atlas_v1_non-neuronal

PURLs:

• https://purl.brain-bican.org/taxonomy/CCN202210140/CS202210140_neurons.json
• https://purl.brain-bican.org/taxonomy/CCN202210140/CS202210140_non-neuronal.json