From 5be9e3c2e9704fe175122eaca856080ece8d3945 Mon Sep 17 00:00:00 2001 From: surangak Date: Fri, 3 Aug 2018 15:32:55 -0400 Subject: [PATCH 1/4] PRN fixes --- negex.python/Annotations-1-120.txt | 4 ++++ negex.python/negex_triggers.txt | 2 ++ 2 files changed, 6 insertions(+) diff --git a/negex.python/Annotations-1-120.txt b/negex.python/Annotations-1-120.txt index 798c519..588cba3 100755 --- a/negex.python/Annotations-1-120.txt +++ b/negex.python/Annotations-1-120.txt @@ -2375,3 +2375,7 @@ Report No. Concept Sentence Negation 119 ABDOMEN: 1. NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY. Affirmed 119 CIRRHOTIC MORPHOLOGY OF THE LIVER AND SMALL UPPER ABDOMINAL LYMPH NODES ARE LIKELY THE SEQUELA OF CHRONIC UNDERLYING LIVER DISEASE CIRRHOTIC MORPHOLOGY OF THE LIVER AND SMALL UPPER ABDOMINAL LYMPH NODES ARE LIKELY THE SEQUELA OF CHRONIC UNDERLYING LIVER DISEASE. Affirmed 119 PELVIS: NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY PELVIS: NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY. Affirmed +2 vomiting PRN for vomiting. Negated +2 vomiting prn for vomiting. Negated +2 vomiting P.R.N. for vomiting. Negated +2 vomiting P.R.N for vomiting. Negated \ No newline at end of file diff --git a/negex.python/negex_triggers.txt b/negex.python/negex_triggers.txt index b9f3712..6f61870 100755 --- a/negex.python/negex_triggers.txt +++ b/negex.python/negex_triggers.txt @@ -63,6 +63,8 @@ not reveal [PREN] not see [PREN] not to be [PREN] patient was not [PREN] +PRN for [PREN] +P.R.N. for [PREN] rather than [PREN] resolved [PREN] test for [PREN] From 2db90aca48038a7757ab7e48a856e48854bf0431 Mon Sep 17 00:00:00 2001 From: surangak Date: Sun, 5 Aug 2018 16:52:29 -0400 Subject: [PATCH 2/4] more fixes --- GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt | 2 ++ negex.python/Annotations-1-120.txt | 8 ++++---- .../06252012/src/pyConTextNLP/pyConTextGraph/itemData.py | 3 ++- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt b/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt index b9f3712..6f61870 100755 --- a/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt +++ b/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt @@ -63,6 +63,8 @@ not reveal [PREN] not see [PREN] not to be [PREN] patient was not [PREN] +PRN for [PREN] +P.R.N. for [PREN] rather than [PREN] resolved [PREN] test for [PREN] diff --git a/negex.python/Annotations-1-120.txt b/negex.python/Annotations-1-120.txt index 588cba3..5e540ca 100755 --- a/negex.python/Annotations-1-120.txt +++ b/negex.python/Annotations-1-120.txt @@ -2375,7 +2375,7 @@ Report No. Concept Sentence Negation 119 ABDOMEN: 1. NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY. Affirmed 119 CIRRHOTIC MORPHOLOGY OF THE LIVER AND SMALL UPPER ABDOMINAL LYMPH NODES ARE LIKELY THE SEQUELA OF CHRONIC UNDERLYING LIVER DISEASE CIRRHOTIC MORPHOLOGY OF THE LIVER AND SMALL UPPER ABDOMINAL LYMPH NODES ARE LIKELY THE SEQUELA OF CHRONIC UNDERLYING LIVER DISEASE. Affirmed 119 PELVIS: NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY PELVIS: NO FINDINGS TO SUGGEST FDG AVID MALIGNANCY. Affirmed -2 vomiting PRN for vomiting. Negated -2 vomiting prn for vomiting. Negated -2 vomiting P.R.N. for vomiting. Negated -2 vomiting P.R.N for vomiting. Negated \ No newline at end of file +120 vomiting PRN for vomiting. Negated +120 vomiting prn for vomiting. Negated +120 vomiting P.R.N. for vomiting. Negated +120 vomiting P.R.N for vomiting. Negated \ No newline at end of file diff --git a/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py b/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py index 1df3cfa..7c06db9 100644 --- a/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py +++ b/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py @@ -107,7 +107,8 @@ def extend(self,iterable): probableNegations = itemData( -["can rule out","PROBABLE_NEGATED_EXISTENCE","","forward"], +["PRN for","PROBABLE_NEGATED_EXISTENCE","","forward"], +["P.R.N. for","PROBABLE_NEGATED_EXISTENCE","","forward"], ["cannot be excluded","PROBABLE_NEGATED_EXISTENCE",r"""cannot\sbe\s((entirely|completely)\s)?(excluded|ruled out)""","backward"], ["is not excluded","PROBABLE_NEGATED_EXISTENCE",r"""(is|was|are|were)\snot\sexcluded""",'backward'], ["adequate to rule the patient out against","PROBABLE_NEGATED_EXISTENCE","","forward"], From b295f9b3df1fdc8fb722dc9ec3e68238332b1872 Mon Sep 17 00:00:00 2001 From: surangak Date: Sun, 5 Aug 2018 16:57:49 -0400 Subject: [PATCH 3/4] fixes --- pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py | 3 +++ .../tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py | 1 + 2 files changed, 4 insertions(+) diff --git a/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py b/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py index dec7853..637eebc 100755 --- a/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py +++ b/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py @@ -64,6 +64,9 @@ def extend(self,iterable): super(itemData,self).extend(iterable) probableNegations = itemData([ +["PRN for","PROBABLE_NEGATED_EXISTENCE","","forward"], +["P.R.N. for","PROBABLE_NEGATED_EXISTENCE","","forward"], +["can rule out","PROBABLE_NEGATED_EXISTENCE","","forward"], ["can rule out","PROBABLE_NEGATED_EXISTENCE","","forward"], ["cannot be excluded","PROBABLE_NEGATED_EXISTENCE",r"""(cannot|can\snot)\sbe\sexcluded""","backward"], ["is not excluded","PROBABLE_NEGATED_EXISTENCE",r"""(is|was|are|were)\snot\sexcluded""",'backward'], diff --git a/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py b/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py index 7c06db9..97bf679 100644 --- a/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py +++ b/pyConTextNLP/tags/06252012/src/pyConTextNLP/pyConTextGraph/itemData.py @@ -109,6 +109,7 @@ def extend(self,iterable): probableNegations = itemData( ["PRN for","PROBABLE_NEGATED_EXISTENCE","","forward"], ["P.R.N. for","PROBABLE_NEGATED_EXISTENCE","","forward"], +["can rule out","PROBABLE_NEGATED_EXISTENCE","","forward"], ["cannot be excluded","PROBABLE_NEGATED_EXISTENCE",r"""cannot\sbe\s((entirely|completely)\s)?(excluded|ruled out)""","backward"], ["is not excluded","PROBABLE_NEGATED_EXISTENCE",r"""(is|was|are|were)\snot\sexcluded""",'backward'], ["adequate to rule the patient out against","PROBABLE_NEGATED_EXISTENCE","","forward"], From 2a4ac3cb0217153c424d0d244eafcdefa8a07c6d Mon Sep 17 00:00:00 2001 From: surangak Date: Sun, 5 Aug 2018 17:00:26 -0400 Subject: [PATCH 4/4] fixes --- pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py b/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py index 637eebc..6656d81 100755 --- a/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py +++ b/pyConTextNLP/tags/06252012/src/pyConTextNLP/itemData.py @@ -67,7 +67,6 @@ def extend(self,iterable): ["PRN for","PROBABLE_NEGATED_EXISTENCE","","forward"], ["P.R.N. for","PROBABLE_NEGATED_EXISTENCE","","forward"], ["can rule out","PROBABLE_NEGATED_EXISTENCE","","forward"], -["can rule out","PROBABLE_NEGATED_EXISTENCE","","forward"], ["cannot be excluded","PROBABLE_NEGATED_EXISTENCE",r"""(cannot|can\snot)\sbe\sexcluded""","backward"], ["is not excluded","PROBABLE_NEGATED_EXISTENCE",r"""(is|was|are|were)\snot\sexcluded""",'backward'], ["adequate to rule the patient out against","PROBABLE_NEGATED_EXISTENCE","","forward"],