Add renal pelvis to AS for kidney

[andreasbueckle]

For the kidney (4 sites), the WUSTL team registered all sites into the renal pelvis, which is a LANDMARK, and hence we get no collisions when landmarks are turned off (it is a cavity):

Same view with landmarks on (the site now lies neatly in the renal pelvis landmark):

View of the renal pelvis landmark in Babylon (with BB):

A solution for this issue could be to make the renal pelvis a crosswalked AS that gets picked up by the mesh and BB collisions. For this, it needs an UBERON or FMA ID. There exists one for it at https://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0036295. Details are TBD. Unsure how to proceed in a timely manner since we have a way to go before the next release where the 3D Reference Object and asct-b-3d-models ​crosswalk (https://lod.humanatlas.io/ref-organ/asct-b-3d-models-crosswalk/latest/) can be adjusted if that is the route we want to go.

As of now, we need to drop 61 datasets:
HBM455.PRVR.965: 2 datasets
HBM486.QXHD.874: 4 datasets
HBM556.CFNP.485: 52 datasets
HBM752.DHVB.758: 3 datasets
So total of 61

[emquardokus]

@andreasbueckle tissue blocks can be taken from the wall of the renal pelvis but you will not get cells from a hole/cavity.
So if the blocks are in the center of the renal pelvis (the center of the tube), they are not correctly registered and those should be confirmed to be actually from renal pelvis and not meant to be in the adjacent kidney tissue next to the renal pelvis. I've not see datasets nor have I heard of any sampling from the renal pelvis from the kidney team.
Urothelial cells line the renal pelvis.
Renal pelvis is contiguous with the ureter in a similar manner to large blood vessels narrow to smaller diameter blood vessels.
Please verify that the wall of renal pelvis were really sampled. I think this is a mistake.

[andreasbueckle]

@Qaurooni, ***@***.***> Could you please ask Amanda?

…

---------------------------------------------- Best, Andreas Andreas "Andi" Bueckle, Ph.D. Research Lead, Cyberinfrastructure for Network Science Center (CNS) Faculty Advisor, Sailing Club at Indiana University US Sailing Certified Race Official Room #4024 Luddy School of Informatics, Computing, and Engineering, Indiana University 700 N Woodlawn Ave (Luddy Hall) 47408 Bloomington, IN - USA email: ***@***.******@***.***> web: www.andreas-bueckle.com<https://www.andreas-bueckle.com/>

________________________________ From: emquardokus ***@***.***> Sent: Thursday, October 3, 2024 6:42:47 PM To: x-atlas-consortia/hra-pop ***@***.***> Cc: Bueckle, Andreas ***@***.***>; Mention ***@***.***> Subject: Re: [x-atlas-consortia/hra-pop] Add renal pelvis to AS for kidney (Issue #112) @andreasbueckle<https://github.com/andreasbueckle> tissue blocks can be taken from the wall of the renal pelvis but you will not get cells from a hole/cavity. So if the blocks are in the center of the renal pelvis (the center of the tube), they are not correctly registered and those should be confirmed to be actually from renal pelvis and not meant to be in the adjacent kidney tissue next to the renal pelvis. I've not see datasets nor have I heard of any sampling from the renal pelvis from the kidney team. Urothelial cells line the renal pelvis. Renal pelvis is contiguous with the ureter in a similar manner to large blood vessels narrow to smaller diameter blood vessels. Please verify that the wall of renal pelvis were really sampled. I think this is a mistake. — Reply to this email directly, view it on GitHub<#112 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AFODRNR2KKL6WU44TASQRY3ZZXB6PAVCNFSM6AAAAABON6VHCSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJSGQ3DEOJTGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[emquardokus]

@danqaurooni tagging you on this as I think Andi did not get your github tag correct. Do you know whether the renal pelvis block are really meant to be within the kidney itself or sampling the wall of renal pelvis? Renal pelvis is a cavity and does not inherently contain cells. The wall of it would that makes up the cavity. Or more probably the blocks which result in 61 datasets are meant to be within the kidney proper.

[danqaurooni]

Amanda told me that the four HuBMAP samples above are all pelvis samples. Quote: "I see where they appear outside of the kidney however, I registered them there because when the renal pelvis landmark is increased they are within those borders." So it seems to me that registering them in the kidney was a mistake to begin with. Should I tell her to re-register them in the pelvis instead?

[emquardokus]

Amanda told me that the four HuBMAP samples above are all pelvis samples. Quote: "I see where they appear outside of the kidney however, I registered them there because when the renal pelvis landmark is increased they are within those borders." So it seems to me that registering them in the kidney was a mistake to begin with. Should I tell her to re-register them in the pelvis instead?

@danqaurooni we needed to verify that the tissue blocks were indeed meant to be registered in the renal pelvis as currently renal pelvis is NOT an RUI organ, it is ONLY a landmark and therefore blocks can not be registered to it. With that in mind, this means we need to export the renal pelvis for both Male and Female as RUI organs, not just landmark organs and add them to our model library and crosswalk. We can see if we can get this part done for 8th HRA release coming up. Thanks for confirming the need.