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Flat stomach #151

Merged
merged 14 commits into from
Jul 13, 2021
Merged

Flat stomach #151

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f134b23
Correct code to remove scale factors related logger errors
mlin865 May 7, 2021
775da09
Merge remote-tracking branch 'abi/master' into flatStomach
mlin865 May 12, 2021
4ccac36
Merge remote-tracking branch 'abi/master' into flatStomach
mlin865 May 23, 2021
01a437a
Add split coordinates
mlin865 Jun 28, 2021
07f0d84
Hide use cross derivatives option
mlin865 Jun 28, 2021
ff910c5
Add mouse stomach
mlin865 Jun 29, 2021
26d8998
Add parameterSet for Mouse 2
mlin865 Jul 1, 2021
23496d1
Add annotation groups on split margin needed for fitting flat scaffold
mlin865 Jul 2, 2021
41457b1
Move markers to dorsal side
mlin865 Jul 2, 2021
6568f06
Replace mouse 1 with mouse 2 and remove redundant parameter set
mlin865 Jul 7, 2021
66ef3ce
Merge remote-tracking branch 'abi/main' into flatStomach
mlin865 Jul 7, 2021
c20bc6f
Make esophagus bigger in Mouse 1
mlin865 Jul 7, 2021
a807de3
Update elements around ostium to be consistent with elements around e…
mlin865 Jul 12, 2021
7999a63
Fix error related to scale factor at annulus
mlin865 Jul 13, 2021
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16 changes: 15 additions & 1 deletion src/scaffoldmaker/annotation/stomach_terms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,23 +4,37 @@

# convention: preferred name, preferred id, followed by any other ids and alternative names
stomach_terms = [
( "antrum on serosa split margin", "None"),
( "body of stomach", "UBERON:0001161", " FMA:14560", "ILX:0724929"),
( "body on serosa split margin", "None"),
( "cardia of stomach", "UBERON:0001162", " FMA:14561", "ILX:0729096"),
( "dorsal stomach", "None"),
( "duodenum", "UBERON:0002114", " FMA:7206", "ILX:0726125"),
( "duodenum on greater curvature", "None"),
( "esophagus", "UBERON:0001043", "FMA: 7131", "ILX:0735017"),
( "esophagus on serosa split margin", "None"),
( "esophagogastric junction", "UBERON:0007650", "FMA: 9434", "ILX:0733910"),
( "forestomach-glandular stomach junction", "UBERON:0012270", "ILX:0729974"),
( "forestomach-glandular stomach junction on inner wall", "None"),
( "forestomach-glandular stomach junction on outer wall", "None"),
( "fundus of stomach", "UBERON:0001160", " FMA:14559", "ILX:0724443"),
( "fundus on serosa split margin", "None"),
( "gastro-esophagal junction on lesser curvature", "None"),
#( "greater curvature of stomach", "UBERON:0001164", "FMA: 14574", "ILX:0724395"),
( "junction between fundus and body on greater curvature", "None"),
# ( "lesser curvature of stomach", "UBERON:0001163", "FMA: 14572", "ILX:0733753"),
( "limiting ridge on greater curvature", "None"),
( "mucosa of stomach", "UBERON:0001199", "FMA:14907", "ILX:0736669"),
( "pylorus", "UBERON:0001166", " FMA:14581", "ILX:0734150"),
( "pyloric antrum", "UBERON:0001165", " FMA:14579", "ILX:0728672"),
( "pylorus on greater curvature", "None"),
( "stomach", "UBERON:0000945", "FMA:7148", "ILX:0736697")
( "pylorus on serosa split margin", "None"),
( "serosa of dorsal stomach", "None"),
( "serosa of stomach", "UBERON:0001201", "FMA:14914", "ILX:0735818"),
( "serosa split margin", "None"),
( "serosa of ventral stomach", "None"),
( "stomach", "UBERON:0000945", "FMA:7148", "ILX:0736697"),
( "ventral stomach", "None"),
]

def get_stomach_term(name : str):
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