Merge pull request #200 from rchristie/lung2_grc

Lung 2 scaffold
ABI-Software · Jul 6, 2022 · ba50d90 · ba50d90
2 parents 07fcb83 + 715d283
commit ba50d90
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Showing 8 changed files with 3,443 additions and 19 deletions.
diff --git a/src/scaffoldmaker/annotation/lung_terms.py b/src/scaffoldmaker/annotation/lung_terms.py
@@ -4,30 +4,84 @@
 
 # convention: preferred name, preferred id, followed by any other ids and alternative names
 lung_terms = [
-    ("apex of right lung accessory lobe", "ILX:0778119"),
+    ("anterior border of left lung", "ILX:0793130"),
+    ("anterior border of right lung", "ILX:0793129"),
+    ("anterior mediastinum of left lung", "ILX:0793183"),
+    ("anterior mediastinum of right lung", "ILX:0793184"),
     ("apex of left lung", "ILX:0778112"),
     ("apex of right lung", "ILX:0778113"),
+    ("apex of right lung accessory lobe", "ILX:0778119"),
+    ("base of left lung surface", "ILX:0793187"),
+    ("base of lower lobe of left lung surface", "ILX:0793577"),
+    ("base of upper lobe of left lung surface", "ILX:0793578"),
+    ("base of right lung accessory lobe surface", "ILX:0793189"),
+    ("base of right lung surface", "ILX:0793188"),
+    ("base of lower lobe of right lung surface", "ILX:0793579"),
+    ("base of middle lobe of right lung surface", "ILX:0793580"),
+    ("dorsal apex of right lung accessory lobe", "ILX:0793603"),
     ("dorsal base of right lung accessory lobe", "ILX:0778125"),
     ("dorsal base of left lung", "ILX:0778126"),
     ("dorsal base of right lung", "ILX:0778127"),
+    ("dorsal surface of right lung accessory lobe", "ILX:0793609"),
     ("horizontal fissure of right lung", "ILX:0746327"),
+    ("horizontal fissure of lower lobe of right lung", "ILX:0793581"),
+    ("horizontal fissure of middle lobe of right lung", "ILX:0793582"),
+    ("horizontal fissure of upper lobe of right lung", "ILX:0793583"),
     ("laterodorsal tip of middle lobe of right lung", "ILX:0778124"),
+    ("lateral surface of left lung", "ILX:0793601"),
+    ("lateral surface of right lung", "ILX:0793602"),
+    ("lateral surface of lower lobe of left lung", "ILX:0793584"),
+    ("lateral surface of lower lobe of right lung", "ILX:0793585"),
+    ("lateral surface of middle lobe of right lung", "ILX:0793586"),
+    ("lateral surface of upper lobe of left lung", "ILX:0793587"),
+    ("lateral surface of upper lobe of right lung", "ILX:0793588"),
+    ("left dorsal base of right lung accessory lobe", "ILX:0793607"),
     ("left lung", "UBERON:0002168", "ILX:0733450"),
+    ("left lung surface", "ILX:0793186"),
+    ("left surface of right lung accessory lobe", "ILX:0793611"),
+    ("left ventral base of right lung accessory lobe", "ILX:0793605"),
     ("lower lobe of left lung", "UBERON:0008953", "ILX:0735534"),
+    ("lower lobe of left lung surface", "ILX:0793192"),
     ("lower lobe of right lung", "UBERON:0002171", "ILX:0725712"),
+    ("lower lobe of right lung surface", "ILX:0793191"),
     ("lung", "UBERON:0002048", "ILX:0726937"),
+    ("medial surface of left lung", "ILX:0793599"),
+    ("medial surface of right lung", "ILX:0793600"),
+    ("medial surface of lower lobe of left lung", "ILX:0793589"),
+    ("medial surface of lower lobe of right lung", "ILX:0793590"),
+    ("medial surface of middle lobe of right lung", "ILX:0793591"),
+    ("medial surface of upper lobe of left lung", "ILX:0793592"),
+    ("medial surface of upper lobe of right lung", "ILX:0793593"),
     ("middle lobe of right lung", "UBERON:0002174", "ILX:0733737"),
+    ("middle lobe of right lung surface", "ILX:0793193"),
     ("medial base of left lung", "ILX:0778120"),
     ("medial base of right lung", "ILX:0778121"),
+    ("anterior mediastinum of left lung", "UBERON:0008820", "ILX:0725455"),
+    ("anterior mediastinum of right lung", "UBERON:0008820", "ILX:0725455"),
     ("oblique fissure of left lung", "ILX:0778115"),
+    ("oblique fissure of lower lobe of left lung", "ILX:0793594"),
+    ("oblique fissure of upper lobe of left lung", "ILX:0793595"),
     ("oblique fissure of right lung", "ILX:0778114"),
+    ("oblique fissure of lower lobe of right lung", "ILX:0793596"),
+    ("oblique fissure of middle lobe of right lung", "ILX:0793597"),
+    ("oblique fissure of upper lobe of right lung", "ILX:0793598"),
+    ("right dorsal base of right lung accessory lobe", "ILX:0793608"),
     ("right lung", "UBERON:0002167", "ILX:0729582"),
+    ("right lung surface", "ILX:0793185"),
     ("right lung accessory lobe", "UBERON:0004890", "ILX:0728696"),
+    ("right lung accessory lobe surface", "ILX:0793190"),
+    ("right surface of right lung accessory lobe", "ILX:0793612"),
+    ("right ventral base of right lung accessory lobe", "ILX:0793606"),
     ("upper lobe of left lung", "UBERON:0008952", "ILX:0735339"),
+    ("upper lobe of left lung surface", "ILX:0793194"),
     ("upper lobe of right lung", "UBERON:0002170", "ILX:0728821"),
+    ("upper lobe of right lung surface", "ILX:0793195"),
+    ("ventral apex of right lung accessory lobe", "ILX:0793604"),
     ("ventral base of right lung accessory lobe", "ILX:0778123"),
     ("ventral base of left lung", "ILX:0778118"),
-    ("ventral base of right lung", "ILX:0778122")
+    ("ventral base of right lung", "ILX:0778122"),
+    ("ventral surface of right lung accessory lobe", "ILX:0793610")
+
 ]
 
 def get_lung_term(name : str):