Open andreasbueckle opened 1 month ago
@katyb
@bherr2 and I talked; Separating AS cell summaries by sceneGraphNode
(aka renal_pyramid_a
, renal_pyramid_b
, etc.) introduces challenges when computing cell summaries and is only relevant for 4-5 AS where multiple 3D meshes share an ontology ID. We should discuss this in a meeting to see if it is worth the change to our process. Additionally, this reduces the amount of data per AS (now bucketed an additional time).
How many AS have this issue?
AS-a | Dataset IDs // maybe they are all the same? AS-b
K
From: Andreas Bueckle @.> Sent: Friday, July 26, 2024 11:15 AM To: x-atlas-consortia/hra-pop @.> Cc: Borner, Katy @.>; Mention @.> Subject: Re: [x-atlas-consortia/hra-pop] Consider separating as-cell-summaries by sceneGraphNode (Issue #96)
@katybhttps://github.com/katyb @bherr2https://github.com/bherr2 and I talked; Separating AS cell summaries by sceneGraphNode (aka renal_pyramid_a, renal_pyramid_b, etc.) introduces challenges when computing cell summaries and is only relevant for 4-5 AS where multiple 3D meshes share an ontology ID. We should discuss this in a meeting to see if it is worth the change to our process. Additionally, this reduces the amount of data per AS (now bucketed an additional time).
— Reply to this email directly, view it on GitHubhttps://github.com/x-atlas-consortia/hra-pop/issues/96#issuecomment-2252976864, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAP6S77DZYHPKOZAZWEDVXLZOJRX5AVCNFSM6AAAAABLNCACHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJSHE3TMOBWGQ. You are receiving this because you were mentioned.Message ID: @.**@.>>
Here is a CSV with as3d | ontology_id | sex | ref_organ: https://github.com/cns-iu/hra-cell-type-populations-supporting-information/blob/main/validations/TEMP/output/as3d_uberon_sex.csv
Code to produce it using SPARQL: https://github.com/cns-iu/hra-cell-type-populations-supporting-information/blob/main/validations/TEMP/make_table_as3d_uberon_sex.ipynb
@bherr2 @katyb suggested that we should bucket as-cell-summaries by individual nodes/meshes who share an UBERON ID to make full usage of the precise RUI registrations. Let's discuss?