Stomach layers

src/scaffoldmaker/annotation/bladder_terms.py

@@ -44,13 +44,14 @@
     ("urethra junction of ventral bladder neck", "ILX:0738410")
 ]
 
-def get_bladder_term(name : str):
+
+def get_bladder_term(name: str):
     """
     Find term by matching name to any identifier held for a term.
     Raise exception if name not found.
     :return ( preferred name, preferred id )
     """
     for term in bladder_terms:
         if name in term:
-            return ( term[0], term[1] )
+            return (term[0], term[1])
     raise NameError("Bladder annotation term '" + name + "' not found.")

src/scaffoldmaker/annotation/colon_terms.py

@@ -4,35 +4,36 @@
 
 # convention: preferred name, preferred id, followed by any other ids and alternative names
 colon_terms = [
-    ( "ascending colon", "UBERON:0001156", "FMA:14545", "ILX:0734393"),
-    ( "descending colon", "UBERON:0001158", "FMA:14547", "ILX:0724444"),
-    ( "caecum", "UBERON:0001153", "FMA:14541", "ILX:0732270"),
-    ( "circular muscle layer of colon", "ILX:0772428"),
-    ( "colon", "UBERON:0001155", "FMA:14543", "ILX:0736005"),
-    ( "colonic mucosa", "UBERON:0000317", "FMA:14984", "ILX:0731046"),
-    ( "distal colon", "UBERON:0008971", "ILX:0727523"),
-    ( "longitudinal muscle layer of colon", "ILX:0775554"),
-    ( "luminal surface of the colonic mucosa", "ILX:0793083"),
-    ( "mesenteric zone", "None"),
-    ( "non-mesenteric zone", "None"),
-    ( "proximal colon", "UBERON:0008972", "ILX:0733240"),
-    ( "serosa of colon", "UBERON:0003335", "FMA:14990", "ILX:0736932"),
-    ( "spiral colon", "UBERON:0010239", "ILX:0735018"),
-    ( "submucosa of colon", "UBERON:0003331", "FMA:14985", "ILX:0728041"),
-    ( "taenia coli", "UBERON:0012419", "FMA:15041", "ILX:0731555"),
-    ( "taenia libera", "ILX:0739285"),
-    ( "taenia mesocolica", "ILX:0739284"),
-    ( "taenia omentalis", "ILX:0739286"),
-    ( "transverse colon", "UBERON:0001157", "FMA:14546", "ILX:0728767")
+    ("ascending colon", "UBERON:0001156", "FMA:14545", "ILX:0734393"),
+    ("descending colon", "UBERON:0001158", "FMA:14547", "ILX:0724444"),
+    ("caecum", "UBERON:0001153", "FMA:14541", "ILX:0732270"),
+    ("circular muscle layer of colon", "ILX:0772428"),
+    ("colon", "UBERON:0001155", "FMA:14543", "ILX:0736005"),
+    ("colonic mucosa", "UBERON:0000317", "FMA:14984", "ILX:0731046"),
+    ("distal colon", "UBERON:0008971", "ILX:0727523"),
+    ("longitudinal muscle layer of colon", "ILX:0775554"),
+    ("luminal surface of the colonic mucosa", "ILX:0793083"),
+    ("mesenteric zone", "None"),
+    ("non-mesenteric zone", "None"),
+    ("proximal colon", "UBERON:0008972", "ILX:0733240"),
+    ("serosa of colon", "UBERON:0003335", "FMA:14990", "ILX:0736932"),
+    ("spiral colon", "UBERON:0010239", "ILX:0735018"),
+    ("submucosa of colon", "UBERON:0003331", "FMA:14985", "ILX:0728041"),
+    ("taenia coli", "UBERON:0012419", "FMA:15041", "ILX:0731555"),
+    ("taenia libera", "ILX:0739285"),
+    ("taenia mesocolica", "ILX:0739284"),
+    ("taenia omentalis", "ILX:0739286"),
+    ("transverse colon", "UBERON:0001157", "FMA:14546", "ILX:0728767")
     ]
 
-def get_colon_term(name : str):
+
+def get_colon_term(name: str):
     """
     Find term by matching name to any identifier held for a term.
     Raise exception if name not found.
     :return ( preferred name, preferred id )
     """
     for term in colon_terms:
         if name in term:
-            return ( term[0], term[1] )
+            return (term[0], term[1])
     raise NameError("Colon annotation term '" + name + "' not found.")

src/scaffoldmaker/annotation/smallintestine_terms.py

@@ -4,19 +4,20 @@
 
 # convention: preferred name, preferred id, followed by any other ids and alternative names
 smallintestine_terms = [
-    ( "duodenum", "UBERON:0002114", "FMA:7206", "ILX:0726125"),
-    ( "ileum", "UBERON:0002116", "FMA:7208", "ILX:0728151"),
-    ( "jejunum", "UBERON:0002115", "FMA:7207", "ILX:0724224"),
-    ( "small intestine", "UBERON:0002108", "FMA:7200", "ILX:0726770")
+    ("duodenum", "UBERON:0002114", "FMA:7206", "ILX:0726125"),
+    ("ileum", "UBERON:0002116", "FMA:7208", "ILX:0728151"),
+    ("jejunum", "UBERON:0002115", "FMA:7207", "ILX:0724224"),
+    ("small intestine", "UBERON:0002108", "FMA:7200", "ILX:0726770")
     ]
 
-def get_smallintestine_term(name : str):
+
+def get_smallintestine_term(name: str):
     """
     Find term by matching name to any identifier held for a term.
     Raise exception if name not found.
     :return ( preferred name, preferred id )
     """
     for term in smallintestine_terms:
         if name in term:
-            return ( term[0], term[1] )
+            return (term[0], term[1])
     raise NameError("Small intestine annotation term '" + name + "' not found.")

src/scaffoldmaker/annotation/stomach_terms.py

@@ -4,46 +4,87 @@
 
 # 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"),
-    ( "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"),
+    ("body of stomach", "UBERON:0001161", " FMA:14560", "ILX:0724929"),
+    ("body-antrum junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793127"),
+    ("body-antrum junction along the greater curvature on luminal surface", "ILX:0793128"),
+    ("body-antrum junction along the greater curvature on serosa", "ILX:0793087"),
+    ("cardia of stomach", "UBERON:0001162", " FMA:14561", "ILX:0729096"),
+    ("circular muscle layer of stomach", "ILX:0774731"),
+    ("circular-longitudinal muscle interface of body of stomach along the gastric-omentum attachment", "ILX:0793088"),
+    ("circular-longitudinal muscle interface of dorsal stomach", "ILX:0793089"),
+    ("circular-longitudinal muscle interface of duodenum along the gastric-omentum attachment", "ILX:0793090"),
+    ("circular-longitudinal muscle interface of esophagus along the cut margin", "ILX:0793091"),
+    ("circular-longitudinal muscle interface of fundus of stomach along the gastric-omentum attachment", "ILX:0793092"),
+    ("circular-longitudinal muscle interface of gastroduodenal junction", "ILX:0793093"),
+    ("circular-longitudinal muscle interface of pyloric antrum along the gastric-omentum attachment", "ILX:0793094"),
+    ("circular-longitudinal muscle interface of pyloric canal along the gastric-omentum attachment", "ILX:0793095"),
+    ("circular-longitudinal muscle interface of stomach", "ILX:0793096"),
+    ("circular-longitudinal muscle interface of ventral stomach", "ILX:0793097"),
+    ("dorsal stomach", "ILX:0793086"),
+    ("duodenum", "UBERON:0002114", " FMA:7206", "ILX:0726125"),
+    ("esophagogastric junction", "UBERON:0007650", "FMA: 9434", "ILX:0733910"),
+    ("esophagogastric junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793098"),
+    ("esophagogastric junction along the greater curvature on luminal surface", "ILX:0793099"),
+    ("esophagogastric junction along the greater curvature on serosa", "ILX:0793100"),
+    ("esophagogastric junction along the lesser curvature on circular-longitudinal muscle interface", "ILX:0793101"),
+    ("esophagogastric junction along the lesser curvature on luminal surface", "ILX:0793102"),
+    ("esophagogastric junction along the lesser curvature on serosa", "ILX:0793103"),
+    ("esophagus", "UBERON:0001043", "FMA:7131", "ILX:0735017"),
+    ("esophagus mucosa", "UBERON:0002469", "FMA:62996", "ILX:0725079"),
+    ("esophagus smooth muscle circular layer", "UBERON:0009960", "FMA:67605", "ILX:0735992"),
+    ("esophagus smooth muscle longitudinal layer", "UBERON:0009961", "FMA:63573", "ILX:0727608"),
+    ("forestomach-glandular stomach junction", "UBERON:0012270", "ILX:0729974"),
+    ("fundus of stomach", "UBERON:0001160", " FMA:14559", "ILX:0724443"),
+    ("fundus-body junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793104"),
+    ("fundus-body junction along the greater curvature on luminal surface", "ILX:0793105"),
+    ("fundus-body junction along the greater curvature on serosa", "ILX:0793106"),
+    ("gastroduodenal junction", "UBERON:0012650", "FMA:17046", "ILX:0725406"),
+    ("gastroduodenal junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793107"),
+    ("gastroduodenal junction along the greater curvature on luminal surface", "ILX:0793108"),
+    ("gastroduodenal junction along the greater curvature on serosa", "ILX:0793109"),
+    ("gastroduodenal junction along the lesser curvature on circular-longitudinal muscle interface", "ILX:0793110"),
+    ("gastroduodenal junction along the lesser curvature on luminal surface", "ILX:0793111"),
+    ("gastroduodenal junction along the lesser curvature on serosa", "ILX:0793112"),
+    ("limiting ridge along the greater curvature on circular-longitudinal muscle interface", "ILX:0793113"),
+    ("limiting ridge along the greater curvature on luminal surface", "ILX:0793114"),
+    ("limiting ridge along the greater curvature on serosa", "ILX:0793115"),
+    ("limiting ridge on circular-longitudinal muscle interface", "ILX:0793116"),
+    ("limiting ridge on luminal surface", "ILX:0793117"),
+    ("limiting ridge on serosa", "ILX:0793118"),
+    ("longitudinal muscle layer of stomach", "ILX:0772619"),
+    ("luminal surface of body of stomach", "ILX:0793119"),
+    ("luminal surface of cardia of stomach", "ILX:0793120"),
+    ("luminal surface of duodenum", "ILX:0793121"),
+    ("luminal surface of esophagus", "ILX:0793122"),
+    ("luminal surface of fundus of stomach", "ILX:0793123"),
+    ("luminal surface of pyloric antrum", "ILX:0793124"),
+    ("luminal surface of pyloric canal", "ILX:0793125"),
+    ("luminal surface of stomach", "ILX:0793126"),
+    ("mucosa of stomach", "UBERON:0001199", "FMA:14907", "ILX:0736669"),
+    ("pyloric antrum", "UBERON:0001165", " FMA:14579", "ILX:0728672"),
+    ("pyloric canal", "UBERON:0008858", "FMA:14580", "ILX:0735898"),
+    ("serosa of body of stomach", "ILX:0771402"),
+    ("serosa of cardia of stomach", "ILX:0776646"),
+    ("serosa of duodenum", "UBERON:0003336", "FMA:14948", "ILX:0732373"),
+    ("serosa of esophagus", "UBERON:0001975", "FMA:63057", "ILX:0725745"),
+    ("serosa of fundus of stomach", "UBERON:0012503", "FMA:17073", "ILX:0726906"),
+    ("serosa of pyloric antrum", "ILX:0777005"),
+    ("serosa of pyloric canal", "ILX:0775898"),
+    ("serosa of stomach", "UBERON:0001201", "FMA:14914", "ILX:0735818"),
+    ("stomach", "UBERON:0000945", "FMA:7148", "ILX:0736697"),
+    ("submucosa of esophagus", "UBERON:0001972", "FMA:62997", "ILX:0728662"),
+    ("submucosa of stomach", "UBERON:0001200", "FMA:14908", "ILX:0732950"),
+    ("ventral stomach", "ILX:0793085"),
     ]
 
-def get_stomach_term(name : str):
+
+def get_stomach_term(name: str):
     """
     Find term by matching name to any identifier held for a term.
     Raise exception if name not found.
     :return ( preferred name, preferred id )
     """
     for term in stomach_terms:
         if name in term:
-            return ( term[0], term[1] )
+            return (term[0], term[1])
     raise NameError("Stomach annotation term '" + name + "' not found.")