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x-atlas-consortia / hra-pop

HRApop
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Consider separating as-cell-summaries by sceneGraphNode #96

Open andreasbueckle opened 1 month ago

andreasbueckle commented 1 month ago

@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?

andreasbueckle commented 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).

katyb commented 1 month ago

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).

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andreasbueckle commented 1 month ago

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