obophenotype / asct-b_validation

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Kidney cell type relationship harmonisation #30

Open dosumis opened 2 years ago

dosumis commented 2 years ago

Limiting to non immune cells:

n s slabel user_slabel o olabel user_olabel
 1 CL:0000653 glomerular visceral epithelial cell glomerular visceral epithelial cell UBERON:0006852 glomerular visceral epithelium glomerular visceral epithelium
2   CL:1000850 macula densa epithelial cell macula densa epithelial cell UBERON:0001291 thick ascending limb of loop of Henle thick ascending limb of loop of Henle
3 CL:0002201 renal beta-intercalated cell renal beta-intercalated cell UBERON:0001232 collecting duct of renal tubule collecting duct of renal tubule
 4 CL:1001033 Peritubular Capillary Endothelial Cell peritubular capillary endothelial cell UBERON:0012441 endothelium of peritubular capillary endothelium of peritubular capillary
 5 CL:1001318 renal interstitial pericyte renal interstitial pericyte UBERON:0003918 kidney mesenchyme kidney mesenchyme
 6 CL:0000648 kidney granular cell kidney granular cell UBERON:0003918 kidney mesenchyme kidney mesenchyme
 7 CL:1000692 kidney interstitial fibroblast kidney interstitial fibroblast UBERON:0003918 kidney mesenchyme kidney mesenchyme
 8 CL:1000691 kidney interstitial myofibroblast kidney interstitial myofibroblast UBERON:0003918 kidney mesenchyme kidney mesenchyme
 

_Log is from 2022-01-03: https://github.com/hubmapconsortium/ccf-validation-tools/blob/v2022-01-03/logs/class_Kidney_log.tsv_

dosumis commented 2 years ago

For reference in discussion: image

  1. See https://github.com/obophenotype/cell-ontology/issues/1399 & https://github.com/obophenotype/uberon/issues/2230
  2. macula densa partonomy is complex in Uberon- needs further investigation: image
  3. https://github.com/obophenotype/cell-ontology/issues/1400
  4. part relationship in Uberon is to capillary not to the endothelium. This is a very common pattern. How might we fix? 5,7&8: we could make these generic part relationships - possible tangle with terms 'stroma' and 'interstitium' ?
  5. See 5,7&8 - but also, doesn't this make case for ASCT+B tables having juxtaglomerular apparatus?