New cap mesh and renal capsule scaffold

src/scaffoldmaker/annotation/kidney_terms.py

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+"""
+Common resource for kidney annotation terms.
+"""
+
+# convention: preferred name, preferred id, followed by any other ids and alternative names
+kidney_terms = [
+    ("anterior surface of kidney", "UBERON:0035368", "ILX:0724840"),
+    ("anterior surface of left kidney", ""),
+    ("anterior surface of right kidney", ""),
+    ("cortex of kidney", "UBERON:0001225", "ILX:0726853"),
+    ("cortex of left kidney", "ILX:0791219"),
+    ("cortex of right kidney", "ILX:0791182"),
+    ("dorsal surface of kidney", ""),
+    ("dorsal surface of left kidney", ""),
+    ("dorsal surface of right kidney", ""),
+    ("hilum of kidney", "UBERON:0008716", "ILX:0731719"),
+    ("hilum of left kidney", ""),
+    ("hilum of right kidney", ""),
+    ("inferior pole of left kidney", "FMA:15609"),
+    ("inferior pole of right kidney", "FMA:15608"),
+    ("inner medulla of left kidney", "ILX:0784932"),
+    ("inner medulla of right kidney", "ILX:0791193"),
+    ("juxtamedullary cortex", "UBERON:0005271", "ILX:0730126"),
+    ("juxtamedullary cortex surface of kidney", ""),
+    ("juxtamedullary cortex surface of left kidney", ""),
+    ("juxtamedullary cortex surface of right kidney", ""),
+    ("kidney", "UBERON:0002113", "ILX:0735723"),
+    ("kidney capsule", "UBERON:0002015", "ILX:0733912"),
+    ("lateral edge of kidney", ""),
+    ("lateral edge of left kidney", ""),
+    ("lateral edge of right kidney", ""),
+    ("lateral surface of kidney", ""),
+    ("lateral surface of left kidney", ""),
+    ("lateral surface of right kidney", ""),
+    ("left kidney", "UBERON:0004538", "ILX:0725163"),
+    ("left kidney capsule", ""),
+    ("major calyx", "UBERON:0001226", "ILX:0730785"),
+    ("medial edge of kidney", ""),
+    ("medial edge of left kidney", ""),
+    ("medial edge of right kidney", ""),
+    ("medial surface of kidney", ""),
+    ("medial surface of left kidney", ""),
+    ("medial surface of right kidney", ""),
+    ("medulla of left kidney", ""),
+    ("medulla of right kidney", ""),
+    ("minor calyx", "UBERON:0001227", "ILX:0730473"),
+    ("outer medulla of left kidney", ""),
+    ("outer medulla of right kidney", ""),
+    ("renal medulla", "UBERON:0000362", "ILX:0729114"),
+    ("renal pelvis", "UBERON:0001224", "ILX:0723968"),
+    ("renal pyramid", "UBERON:0004200", "ILX:0727514"),
+    ("right kidney", "UBERON:0004539", "ILX:0735697"),
+    ("right kidney capsule", ""),
+    ("posterior surface of kidney", "UBERON:0035471", "ILX:0724479"),
+    ("posterior surface of left kidney", ""),
+    ("posterior surface of right kidney", ""),
+    ("superior pole of left kidney", "FMA:15607"),
+    ("superior pole of right kidney", "FMA:15606"),
+    ("ventral surface of kidney", ""),
+    ("ventral surface of left kidney", ""),
+    ("ventral surface of right kidney", "")
+    ]
+
+def get_kidney_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 kidney_terms:
+        if name in term:
+            return (term[0], term[1])
+    raise NameError("Kidney annotation term '" + name + "' not found.")