Review 1.1 Kidney table log

[dosumis]

Errors WARNING - Unrecognized cell content ''

WARNING - Different labels found for UBERON:0004200. Uberongraph: kidney pyramid ; ASCT+b table: renal pyramid Author gave wrong label for uberon.

WARNING - Different labels found for UBERON:0005750. Uberongraph: glomerular parietal epithelium ; ASCT+b table: glomerular parietal epithelium

ASCT+B table for Author preferred name is "parietal epithelial layer"

WARNING - Different labels found for UBERON:0005125. Uberongraph: metanephric proximal straight tubule ; ASCT+b table: proximal straight tubule segment 3

Author intends http://purl.obolibrary.org/obo/UBERON_0001290 proximal straight tubule which has exact synonym S3

WARNING - Different labels found for UBERON:0001289. Uberongraph: descending limb of loop of Henle ; ASCT+b table: descending thin limb of loop of Henle WARNING - Different labels found for UBERON:0004193. Uberongraph: loop of Henle ascending limb thin segment ; ASCT+b table: ascending thin limb of loop of Henle WARNING - Different labels found for UBERON:0004294. Uberongraph: glomerular capillary endothelium ; ASCT+b table: glomerular capillary endothelium

WARNING - Different labels found for UBERON:0001229. Uberongraph: renal corpuscle ; ASCT+b table: Renal Corpuscle WARNING - Different labels found for UBERON:0004204. Uberongraph: outer medullary collecting duct ; ASCT+b table: renal outer medullary collecting duct WARNING - Different labels found for UBERON:0012441. Uberongraph: endothelium of peritubular capillary ; ASCT+b table: WARNING - Different labels found for UBERON:0005097. Uberongraph: renal connecting tubule ; ASCT+b table: connecting tubule WARNING - Different labels found for UBERON:0004190. Uberongraph: renal glomerulus vasculature ; ASCT+b table: glomerulus vasculature WARNING - Different labels found for UBERON:0001284. Uberongraph: renal column ; ASCT+b table: renal column (column of Bertin)

Tables Raw log output for kidney table

n	s	slabel	user_slabel	o	olabel	user_olabel
1	UBERON:0001284	renal column (column of Bertin)	renal column	UBERON:0000362	renal medulla	renal medulla
2	UBERON:0005096	descending thin limb	descending thin limb of loop of Henle	UBERON:0001289	descending thin limb of loop of Henle	Loop of Henle (Thin Limb)
3	UBERON:0001232	collecting duct of renal tubule	Tubules	UBERON:0004100	renal collecting system	renal collecting system
4	UBERON:0001986	endothelium	Endothelium (non glomerular)	UBERON:0006544	kidney vasculature	Vessels
5	UBERON:0005272	peritubular capillary	Peritubular Capillary	UBERON:0012441		Endothelium/cortex (non glomerular)

[dosumis]

@emquardokus Just posting limited example so we can play with how we document these.

[dosumis]

General notes on reports:

1. We should have a column for name in Uberon as the user entered name doesn't always correspond.

Specific notes on issues:

1. Uberon has 'renal column' 'part of' some 'renal cortex' but also has the textual definition: "A column of tissue that is histologically identical to tissue found in the renal cortex, but which is located in the medulla between the renal pyramids.". This therefore seems to be a modelling issue which will need some discussion to resolve. obophenotype/uberon#2126
2. 1289 - Descending limb of loop of Henle - "proximal part of loop of Henle"; 5096 = 'descending thin limb - "part of the loop of Henle situated just after the proximal straight tubule (S3)". This also looks like a modelling issue to be discussed. obophenotype/asct-b_validation#23
3. 1232 'collecting duct of renal tubule' 4100 'renal collecting system'. This looks like a missing link in Uberon: https://github.com/obophenotype/uberon/issues/2085. FIXED
4. subject class is general endothelium. Perhaps we need a compound term 'endothelium of kidney vasculature?
5. Subject and object accidentally reversed?
   • UBERON:0012441 = 'endothelium of peritubular capillary' = which already has a part relationship to peritubular capillary.

[dosumis]

@emquardokus

Can we prioritise fixing genuine mistakes in the tables. It would be great if we can use this to show progress on harmonization. Issue 5 here falls into that category.

The spreadsheet has AS/4	AS/4/LABEL	AS/4/ID	AS/5	AS/5/LABEL	AS/5/ID
Endothelium/cortex (non glomerular)		UBERON:0012441	Peritubular Capillary	peritubular capillary	UBERON:0005272

UBERON:0012441 = 'endothelium of peritubular capillary' - The order should just be reversed. (the endothelium is part of the capillary, not the other way around). I was hoping fixes like this could be made with authors just being informed rather than asked.

[emquardokus]

@dosumis yes, this was an early review and I'm just going back to these first few now. Added Uberon label for UBERON:0012441 = 'endothelium of peritubular capillary'; I see what you mean on reverse of the peritubulary capillary should be ahead of the epithelium... ; I'll work through kidney thoroughly tonight since tomorrow 10-26-2021 I can speak to the KPMP consortium biocuration committee who has been making all the decisions for their work and constructed their table. Should be able to resolve most if not all tomorrow afternoon 3-4 pm Eastern time meeting.

[emquardokus]

10/26/2021 Changed renal pyramid to kidney pyramid for uberon label; author preferred is renal pyramid.

10/26/2021 Changed UBERON:0005125 metanephric proximal straight tubule to author intended AS/5	AS/5/LABEL	AS/5/ID
proximal straight tubule segment 3	proximal straight tubule	UBERON:0001290

[emquardokus]

11-10-2021 Fixed reversed

n	s	slabel	user_slabel	o	olabel	user_olabel
5	UBERON:0005272	peritubular capillary	Peritubular Capillary	UBERON:0012441		Endothelium/cortex (non glomerular)