Dialogue for selecting syntactic rules improved

.gitignore

@@ -0,0 +1,2 @@
+/TableLists.pyc
+/QueryDBClass.pyc

Data/.gitignore

@@ -0,0 +1,2 @@
+/Table.pyc
+/__init__.pyc

DrugDrugInteraction/HeadersWithAnnotations.sql

@@ -0,0 +1,8 @@
+SELECT idCell,specId,TableOrder,cell.Content,GROUP_CONCAT(AnnotationID SEPARATOR ', ') as concepts,GROUP_CONCAT(AnnotationDescription SEPARATOR ', ') as semanticTypes 
+FROM cell 
+left join cellroles on cell.idCell=cellroles.Cell_idCell 
+left join arttable on arttable.idTable=cell.Table_idTable 
+left join annotation on cell.idCell=annotation.Cell_idCell 
+left join article on article.idArticle=arttable.Article_idArticle 
+where CellRole_idCellRole=1 and section="34073-7" 
+Group by idCell;

DrugDrugInteraction/HeadersWithAnnotationsMetaMapOnly.sql

@@ -0,0 +1,8 @@
+SELECT idCell,specId,TableOrder,cell.Content,GROUP_CONCAT(AnnotationID SEPARATOR ', ') as concepts,GROUP_CONCAT(AnnotationDescription SEPARATOR ', ') as semanticTypes 
+FROM cell 
+left join cellroles on cell.idCell=cellroles.Cell_idCell 
+left join arttable on arttable.idTable=cell.Table_idTable 
+left join annotation on cell.idCell=annotation.Cell_idCell 
+left join article on article.idArticle=arttable.Article_idArticle 
+where CellRole_idCellRole=1 and section="34073-7" and AgentName="MetaMap" 
+Group by idCell;

Projects/AgeExt/Config.cfg

@@ -0,0 +1,5 @@
+Host:127.0.0.1
+Port:3306
+User:root
+Pass:
+Database:table_db

Projects/GetAge/Config.cfg

@@ -0,0 +1,5 @@
+Host:127.0.0.1
+Port:3306
+User:root
+Pass:
+Database:table_db

Projects/Nikola/NewRule/NewRule_BlackList.lst

@@ -0,0 +1,29 @@
+Type:BlackList
+Header:1
+Stub:1
+Super-row:0
+Data:0
+All:0
+WordList:
+\b(p-value)\b
+\b(P)\b
+\b(p)\b
+\b(onset)\b
+\B(≥)\B
+\B(<)\B
+\B(>)\B
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

Projects/Nikola/NewRule/NewRule_WhiteList.lst

@@ -0,0 +1,33 @@
+Type:WhiteList
+Header:0
+Stub:1
+Super-row:1
+Data:0
+All:0
+WordList:
+Age
+age
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

Projects/Nikola/NewRule/Rule.cfg

@@ -0,0 +1,4 @@
+Class:Age
+DefUnit:years
+PosUnit:years,months,days,weeks
+PragClass:BaselineCharacteristic

Projects/Nikola/NewRule/SyntacticRules.sin

@@ -0,0 +1,54 @@
++GetMean1
+(\d+\.*\d*)[?  ]*[\-—–−––,]+(\d+\.*\d*)[ (]*(\d+\.*\d*)[?  ]*[±][?  ]*(\d+\.*\d*)[)]*
+1->range_min
+2->range_max
+3:median,Median->median
+3->mean
+4->SD
++GetMean2
+(\d+\.*\d*)[?  ]*[±][?  ]*(\d+\.*\d*)[ (]*(\d+\.*\d*)[?  ]{0,}[\-—–−––,]+[ ]*(\d+\.*\d*)[)]*
+1:median,Median->median
+1->mean
+2->SD
+3->range_min
+4->range_max
++GetMean4
+(\d+\.*\d*)[?  ]*[\(](\d+\.*\d*)[?  ]{0,}[\-—–−––,]+(\d+\.*\d*)[\)]*
+1:median,Median->median
+1->mean
+2->range_min
+3->range_max
++GetRange1
+(\d+\.*\d*)[?  ]*[(\[](\d+\.*\d*)[?  ]{0,}[\-—–−,]{1,}[?  ]{0,}(\d+\.*\d*)
+1:median,Median->median
+2->range_min
+3->range_max
++GetRange2
+[(](\d+\.*\d*)[?  ]{0,}[\-—–−,;]{1,}[?  ]{0,}(\d+\.*\d*)[)][?  ]*(\d+\.*\d*)
+1->range_min
+2->range_max
+3:median,Median->median
+3->mean
++GetRange21
+(\d+\.*\d*)[?  ]{0,}[\-—–−,;]{1,}[?  ]{0,}(\d+\.*\d*)[,?  ]+(\d+\.*\d*)
+1->range_min
+2->range_max
+3->mean
++GetRange3
+(\d+\.*\d*)[?  ]{0,1}[\-—–−,;to]{1,}[?  ]{0,}(\d+\.*\d*)
+1->range_min
+2->range_max
++GetMean6
+(\d+\.*\d*)[?  ]{0,}[±]{1,}[?  ]{0,}(\d+\.*\d*)
+1:median,Median->median
+1->mean
+2->SD
++GetMean7
+(\d+\.{0,}\d*)[?  ]{0,}[(](\d+\.{0,}\d*)[)]
+1:median,Median->median
+1->mean
+2->SD
++GetMean8
+(\d+\.*\d*)
+1:median,Median->median
+1->mean

Wizard/DefaultSintacticRules/Gender

@@ -1,6 +1,6 @@
 +GetComplexPattern
 (\d+)[ ]*[(](\d+[.]*\d*)[)/ ]+(\d+)[ ]*[(](\d+[.]*\d*)[)]
-1:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem.women,Women,women,females,Females->male
+1:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,women,Women,women,females,Females->male
 1:female,Female,f,F,fem,Fem,women,Women,females,Females;male,m,Male,M,men,Men,males,Males->female
 1->male
 2:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,women,Women,women,females,Females->male perc
@@ -104,4 +104,4 @@ Female: (\d+)[ ][(](\d+)[%][)]
 (\d+)
 1:male,m,Male,M,men,Men,males,Males->male
 1:female,f,Female,F,women,Fem,fem,women,Women,females,Females->female
-1->male
+1->male

Wizard/DefaultSintacticRules/Gender.txt

@@ -0,0 +1,139 @@
++GetComplexPattern
+(\d+)[ ]*[(](\d+[.]*\d*)[)/ ]+(\d+)[ ]*[(](\d+[.]*\d*)[)]
+1:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,women,females,Females->male
+1:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,Males->female
+1->male
+2:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,women,females,Females->male perc
+2:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,Males->female perc
+2->male perc
+3:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,women,Females,females->female
+3:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,Males->male
+3->female
+4:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,women,Females,females->female perc
+4:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,Males->male perc
+4->female perc
++GetWithSymbols
+(\d+)[ ]*[Mm][ ]*[;,:/][ ]*(\d+)[ ]*[Ff]
+1->male
+2->female
++GetWithSymbols2
+(\d+)[ ]*[Ff][ ]*[;,:/][ ]*(\d+)[ ]*[Mm]
+1->female
+2->male
++GetFemalePerc
+(\d+[.]*\d*)[ ]*[%]+[ ]*[(](\d+)[)]
+1:male,Male,m,M,men,Men,males,Males->male percent
+1:Female,female,fem,F,f,Fem,women,Women,females,Females
+->female percent
+2:male,Male,m,men,Men,males,Males->male
+2:Female,female,fem,F,f,Fem,women,Women,females,Females
+->female
++GetPercInBrackets
+(\d*[,]*\d+[.]*\d*)[ ]*[(](\d+[.]*\d*)[)]
+1:male,m,Male,M,men,Men,males,Males->male
+1:female,f,F,fem,Fem,Female,women,Women,Females,females
+->female
+2:male,m,Male,M,men,Men,males,Males->male perc
+2:female,f,F,fem,Fem,Female,women,Women,females,Females
+->female perc
++GetMaleFemale1Perc
+(\d+[.]\d+)[/:\\, ]{1,}(\d+[.]\d+)
+1:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,women,Females,females->male perc
+1:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,Males->female perc
+1->male perc
+2:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,women,females,Females->female perc
+2:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,males->male perc
+2->female perc
++GetPercWOBrackets
+(\d+)[ ]{1,}(\d+[.]*\d*)[%]
+1:male,Male,m,M,men,Men,males,Males->male
+1:female,Female,f,F,fem,Fem,women,Women,females,Females
+->female
+1->male
+2:male,Male,m,M,men,Men,males,Males->male perc
+2:female,Female,f,F,fem,Fem,women,Women,Females,females
+->female perc
+2->female perc
++GetMaleFemale1
+(\d+)[/:\\,  ]{1,}(\d+)
+1:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,females,Females->male
+1:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,Men,men,males,Males->female
+1->male
+2:male,m,Male,M,men,Men,males,Males;female,f,F,fem,Fem,
+women,Women,Females,females->female
+2:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,Men,men,males,males->male
+2->female
++GetMaleFromTxt
+Male:[ ](\d+)[ (]+(\d+)[%]
+1->male
+2->male perc
++GetFemaleFromTxt
+Female[:][ ](\d+)[ (]+(\d+)[%]
+1->female
+2->female perc
++GetMaleFemalePerc
+(\d+[.]*\d*)[/:\\, ]{1,}(\d+[.]*\d*)
+1:male,m,Male,M,Men,men,males,Males;female,f,F,fem,Fem,
+women,Women,females,Females->male perc
+1:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,Men,men,males,Males->female perc
+1->male perc
+2:male,m,Male,M,Men,men,males,Males;female,f,F,fem,Fem,
+women,Women,females,Females->female perc
+2:female,Female,f,F,fem,Fem,women,Women,females,Females;
+male,m,Male,M,men,Men,males,Males->male perc
+2->female perc
++GetMaleFemale2
+(\d+)[ (]{1,}(\d+[.]*\d*)[%]{1,}
+1:male,m,Male,M,men,Men,males,Males->male
+1:female,f,F,Fem,Female,women,Women,females,Females
+->female
+1->total
+2:male,m,Male,M,men,Men,males,Males->male prec
+2:female,f,F,Fem,Female,women,Women,Females,females
+->female perc
+2->female perc
++GetPerc
+(\d+)[ (]{1,}(\d+[.]*\d*){1,}
+1:male,m,Male,M,Men,men,males,Males->male
+1:female,f,F,Fem,Female,women,Women,females,Females
+->female
+1->total
+2:male,m,Male,M,Men,men,males,Males->male perc
+2:female,f,F,Fem,Female,women,Women,females,Females
+->female perc
+2->female perc
++GetMale
+Male: (\d+)[ ][(](\d+)[%][)]
+1->male
+2->male percent
++GetFemale
+Female: (\d+)[ ][(](\d+)[%][)]
+1->female
+2->female percent
++GetNumPerc
+(\d+[.]\d+)
+1:male,m,Male,M,men,Men,males,Males->male perc
+1:female,f,Female,F,women,Fem,fem,Women,women,females,
+Females->female perc
++GetNum
+(\d+)
+1:male,m,Male,M,men,Men,males,Males->male
+1:female,f,Female,F,women,Fem,fem,women,Women,females,
+Females->female
+1->male

Wizard/Projects/GetGender/Config.cfg

@@ -0,0 +1,5 @@
+Host:127.0.0.1
+Port:3306
+User:root
+Pass:
+Database:table_db

Wizard/Projects/GetGender/GetGender/GetGender_BlackList.lst

@@ -0,0 +1,9 @@
+Type:BlackList
+Header:1
+Stub:1
+Super-row:1
+Data:0
+WordList:
+change
+excluded
+

Wizard/Projects/GetGender/GetGender/GetGender_WhiteList.lst

@@ -0,0 +1,10 @@
+Type:WhiteList
+Header:1
+Stub:1
+Super-row:1
+Data:0
+WordList:
+[annID]:C0086287
+[annID]:C0086582
+[annID]:C0804628
+