From 2c13b22eb460a34e8078c3c7f4f9ded2ae2e0028 Mon Sep 17 00:00:00 2001 From: Zohreh Ekhlasi Date: Mon, 14 Jun 2021 16:39:31 +1200 Subject: [PATCH 1/2] updated new terms with ILX. --- src/scaffoldmaker/annotation/bladder_terms.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/scaffoldmaker/annotation/bladder_terms.py b/src/scaffoldmaker/annotation/bladder_terms.py index 920f5d94..7deccd52 100644 --- a/src/scaffoldmaker/annotation/bladder_terms.py +++ b/src/scaffoldmaker/annotation/bladder_terms.py @@ -6,11 +6,11 @@ bladder_terms = [ ("bladder lumen", "UBERON:0009958"), ("dome of the bladder", "ILX:0738433"), - ("dorsal part of bladder lumen", "None"), + ("dorsal part of urinary bladder lumen", "ILX:0777128"), ("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 bladder", "None"), + ("dorsal part of bladder", "ILX:0778155"), ("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"), @@ -27,7 +27,7 @@ ("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 urinary bladder lumen", "ILX:0777129"), ("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"), @@ -35,13 +35,13 @@ ("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 bladder", "None"), + ("ventral part of bladder", "ILX:0778156 "), ("ventral part of urethra", "ILX:0739259"), ("apex of urinary bladder", "ILX:0774405"), - ("left ureter junction with bladder", "None"), - ("right ureter junction with bladder", "None"), - ("urethra junction with bladder dorsal", "None"), - ("urethra junction with bladder ventral", "None") + ("left ureter junction with bladder", "ILX:0778142"), + ("right ureter junction with bladder", "ILX:0778143"), + ("urethra junction of dorsal bladder neck", "ILX:0778154"), + ("urethra junction of ventral bladder neck", "ILX:0738410") ] def get_bladder_term(name : str): From 37e54f071d969f7378d9c3487c54511e6d5534d1 Mon Sep 17 00:00:00 2001 From: Zohreh Ekhlasi Date: Mon, 14 Jun 2021 16:39:53 +1200 Subject: [PATCH 2/2] Changed some annotation terms. --- .../meshtypes/meshtype_3d_bladderurethra1.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py index 1c271c0f..d8d1fcd1 100644 --- a/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py +++ b/src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py @@ -896,8 +896,8 @@ def generateBaseMesh(cls, region, options): apexGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("apex of urinary bladder")) leftUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("left ureter junction with bladder")) rightUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("right ureter junction with bladder")) - dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder dorsal")) - ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder ventral")) + dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction of dorsal bladder neck")) + ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction of ventral bladder neck")) idx1 = 1 xi1 = [0.0, 0.0, 0.0] @@ -1017,11 +1017,11 @@ def defineFaceAnnotations(cls, region, options, annotationGroups): serosaOfBladder_ventral.getMeshGroup(mesh2d).addElementsConditional(is_bladder_serosa_ventral) is_bladder_lumen_dorsal = fm.createFieldAnd(is_urinaryBladder_lumen, is_dorsal_bladder) - lumenOfBladder_dorsal = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("dorsal part of bladder lumen")) + lumenOfBladder_dorsal = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("dorsal part of urinary bladder lumen")) lumenOfBladder_dorsal.getMeshGroup(mesh2d).addElementsConditional(is_bladder_lumen_dorsal) is_bladder_lumen_ventral = fm.createFieldAnd(is_urinaryBladder_lumen, is_ventral_bladder) - lumenOfBladder_ventral = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("ventral part of bladder lumen")) + lumenOfBladder_ventral = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("ventral part of urinary bladder lumen")) lumenOfBladder_ventral.getMeshGroup(mesh2d).addElementsConditional(is_bladder_lumen_ventral) is_body_serosa_dorsal = fm.createFieldAnd(is_body_serosa, is_dorsal_bladder)