NTRs: kidney collecting duct cell types

[GoogleCodeExporter]

To be reverse-engineered from:

[Term]
id: MP:0011754
name: abnormal kidney collecting duct intercalated cell morphology
namespace: MPheno.ontology
def: "any structural anomaly of any of the functionally distinct subtypes of 
cells (alpha or beta) found on the kidney collecting duct epithelium that 
regulate acid-base homeostasis and play an important role in the kidney's 
response to acidosis and alkalosis; alpha-intercalated cells secrete acid 
whereas beta-intercalated cells secrete base; metabolic acidosis results in the 
conversion of beta- cells to alpha-intercalated cells giving the kidney a 
greater ability to secrete protons and return pH to the normal range" [MGI:anna]
is_a: MP:0011843  ! abnormal kidney collecting duct epithelium morphology

[Term]
id: MP:0011755
name: abnormal kidney collecting duct alpha-intercalated cell morphology
namespace: MPheno.ontology
def: "any structural anomaly of the tall, columnar epithelial cells found on 
the kidney collecting duct epithelium which secrete acid (via an apical 
H+-ATPase and H+/K+ exchanger) in the form of hydrogen ions and reabsorb 
bicarbonate (via band 3, a basolateral Cl-/HCO3- exchanger);damage to the 
alpha-intercalated cell's ability to secrete acid can result in distal renal 
tubular acidosis" [MGI:anna]
synonym: " abnormal collecting duct type A intercalated cells" EXACT []
synonym: "abnormal collecting duct alpha-intercalated cells" EXACT []
synonym: "abnormal kidney collecting duct A-type intercalated cells" EXACT []
is_a: MP:0011754  ! abnormal kidney collecting duct intercalated cell morphology

[Term]
id: MP:0011756
name: abnormal kidney collecting duct beta-intercalated cell morphology
namespace: MPheno.ontology
def: "any structural anomaly of the shorter, flatter cells found on the kidney 
collecting duct epithelium which secrete bicarbonate (via pendrin, a 
specialized apical Cl-/HCO3- exchanger) and reabsorb acid (via a basal 
H+-ATPase)" [MGI:anna]
synonym: "abnormal collecting duct beta-intercalated cells" EXACT []
synonym: "abnormal collecting duct type B intercalated cells" EXACT []
synonym: "abnormal kidney collecting duct B-type intercalated cells" EXACT []
is_a: MP:0011754  ! abnormal kidney collecting duct intercalated cell morphology

Original issue reported on code.google.com by cmung...@gmail.com on 15 May 2013 at 8:30

[emquardokus]

@paolaroncaglia we could have someone from Kidney Precision Medicine Project review this. They may have already submitted NTRs for cell types via Todd Valerius. I will look into this more, but flagging this OLD issue to keep open

[paolaroncaglia]

@emquardokus

@paolaroncaglia we could have someone from Kidney Precision Medicine Project review this. They may have already submitted NTRs for cell types via Todd Valerius. I will look into this more, but flagging this OLD issue to keep open

Great, thanks! To keep track, I'll assign this ticket to the two of us (and will modify the labels).

[paolaroncaglia]

Note for self: when I get to this ticket, check if there's any overlap with @emquardokus ' ASCT-B table for kidney.

[paolaroncaglia]

Un-assigning from this ticket for now as I'll probably focus on a separate ASCT+B table. But feel free to re-assign to me if/as needed.

[ghost]

It appears two of the three mentioned cell types exist in CL (as normal variants):

CL:1001432 ‘kidney collecting duct intercalated cell’ CL:4030015 'kidney collecting duct alpha-intercalated cell’

Will assign to self to add new term: kidney collecting duct beta-intercalated cell

[ghost]

Closing this ticket. Remaining task subsumed by https://github.com/obophenotype/cell-ontology/issues/1688.