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Bladder dorsal ventral #120

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merged 10 commits into from
Feb 23, 2021
Merged

Bladder dorsal ventral #120

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ebd9d4e
Added dorsal ventral annotations to the bladder terms.
zekh167 Jan 18, 2021
c914ee5
Added dorsal ventral annotations to the scaffold.
zekh167 Jan 18, 2021
4ed4442
Added marker point.
zekh167 Feb 3, 2021
52a4439
Added ILX for two terms and some minor changes.
zekh167 Feb 9, 2021
1183b0b
Changed two annotation terms based on SciCrunch terminology list.
zekh167 Feb 9, 2021
51d1a3f
Merge remote-tracking branch 'abi/master' into bladder_dorsal_ventral
zekh167 Feb 10, 2021
3528cac
Put terms in alphabetical order.
zekh167 Feb 19, 2021
6fddcb3
changed the way to annotate dorsal and ventral part of bladder and ur…
zekh167 Feb 19, 2021
33871ca
Minor changes in annotation.
zekh167 Feb 22, 2021
79ff779
Minor changes in annotation.
zekh167 Feb 23, 2021
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38 changes: 29 additions & 9 deletions src/scaffoldmaker/annotation/bladder_terms.py
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Expand Up @@ -4,19 +4,39 @@

# convention: preferred name, preferred id, followed by any other ids and alternative names
bladder_terms = [
("urinary bladder", "UBERON:0001255", "FMA:15900"),
("neck of urinary bladder", "UBERON:0001258", "FMA:15912"),
("Dome of the Bladder", "ILX:0738433"),
("serosa of urinary bladder", "UBERON:0001260"),
("bladder lumen", "UBERON:0009958"),
("serosa of body of urinary bladder", "ILX:0739276"),
("dome of the bladder", "ILX:0738433"),
("dorsal part of bladder lumen", "None"),
("dorsal part of lumen of body of urinary bladder", "ILX:0739250"),
("dorsal part of lumen of neck of urinary bladder", "ILX:0739255"),
("dorsal part of lumen of urethra", "ILX:0739260"),
("dorsal part of the bladder", "None"),
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Rename to remove "the" --> "dorsal part of bladder" for consistency with other terms.
Also "ventral part of bladder" below.
(Exception: "dome of the bladder" is already in SciCrunch with "the", so can't change it).

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done.

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Also update where they are used?

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Done Richard.

("dorsal part of urethra", "ILX:0739258"),
("dorsal part of serosa of body of urinary bladder", "ILX:0739278"),
("dorsal part of serosa of neck of urinary bladder", "ILX:0739280"),
("dorsal part of serosa of urethra", "ILX:0739283"),
("dorsal part of serosa of urinary bladder", "ILX:0739248"),
("lumen of body of urinary bladder", "ILX:0739252"),
("serosa of neck of urinary bladder", "ILX:0739277"),
("lumen of neck of urinary bladder", "ILX:0739256"),
("urethra", "UBERON:0000057", "ILX:0733022"),
("lumen of urethra", "ILX:0736762"),
("lumen of urethra", "UBERON:0010390", "ILX:0736762"),
("neck of urinary bladder", "UBERON:0001258", "FMA:15912"),
("serosa of body of urinary bladder", "ILX:0739276"),
("serosa of neck of urinary bladder", "ILX:0739277"),
("serosa of urethra", "ILX:0739282"),
("ureter", "UBERON:0000056", "ILX:0728080")
("serosa of urinary bladder", "UBERON:0001260"),
("ureter", "UBERON:0000056", "ILX:0728080"),
("urethra", "UBERON:0000057", "ILX:0733022"),
("urinary bladder", "UBERON:0001255", "FMA:15900"),
("ventral part of bladder lumen", "None"),
("ventral part of lumen of body of urinary bladder", "ILX:0739251"),
("ventral part of lumen of neck of urinary bladder", "ILX:0739257"),
("ventral part of lumen of urethra", "ILX:0739261"),
("ventral part of serosa of body of urinary bladder", "ILX:0739279"),
("ventral part of serosa of neck of urinary bladder", "ILX:0739281"),
("ventral part of serosa of urethra", "ILX:0739306"),
("ventral part of serosa of urinary bladder", "ILX:0739249"),
("ventral part of the bladder", "None"),
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"ventral part of bladder".

("ventral part of urethra", "ILX:0739259")
]

def get_bladder_term(name : str):
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