WIP #2532 ontogeny factor

Open-Systems-Pharmacology · Jun 14, 2023 · cb29b53 · cb29b53
1 parent f1e3456
commit cb29b53
Show file tree

Hide file tree

Showing 2 changed files with 10,301 additions and 10,248 deletions.
diff --git a/src/Db/Diff/PKSimDB_diff.txt b/src/Db/Diff/PKSimDB_diff.txt
@@ -1,6 +1,24 @@
 INSERT INTO tab_calculation_method_rates(calculation_method,formula_rate,formula,dimension) VALUES('DiseaseStates','PARAM_ChildPughScore','0','Dimensionless');
+INSERT INTO tab_calculation_method_rates(calculation_method,formula_rate,formula,dimension) VALUES('ExpressionParameters','TableFormulaWithXArgument_OntogenyFactor',NULL,'Dimensionless');
+INSERT INTO tab_calculation_method_rates(calculation_method,formula_rate,formula,dimension) VALUES('ExpressionParameters','TableFormulaWithXArgument_OntogenyFactorGI',NULL,'Dimensionless');
+UPDATE tab_calculation_method_rates SET formula='Age * 365.25/7 + GA' WHERE calculation_method='GFR_Calculation' AND formula_rate='PARAM_PostMenstrualAge';
+INSERT INTO tab_calculation_method_rates(calculation_method,formula_rate,formula,dimension) VALUES('Individual_PKSim','PARAM_PostMenstrualAge','Age + GA * 7/365.25','Age in years');
 INSERT INTO tab_container_names(container_type,container_name,display_name,description,extension,sequence,icon_name) VALUES('DISEASE_STATE','HI','HI Parameter container','HI Parameter container',NULL,1,NULL);
+INSERT INTO tab_container_parameter_rates(container_id,container_type,container_name,parameter_name,calculation_method,formula_rate,min_value,min_isallowed,max_value,max_isallowed,value_origin) VALUES(146,'ORGANISM','Organism','Post menstrual age','Individual_PKSim','PARAM_PostMenstrualAge',0.0,1,NULL,1,NULL);
+UPDATE tab_container_parameter_rates SET formula_rate='TableFormulaWithXArgument_OntogenyFactor' WHERE container_id=5015 AND container_type='GENERAL' AND container_name='PROTEIN' AND parameter_name='Ontogeny factor' AND calculation_method='ExpressionParameters';
+UPDATE tab_container_parameter_rates SET formula_rate='TableFormulaWithXArgument_OntogenyFactorGI' WHERE container_id=5015 AND container_type='GENERAL' AND container_name='PROTEIN' AND parameter_name='Ontogeny factor GI' AND calculation_method='ExpressionParameters';
+INSERT INTO tab_container_parameter_rates(container_id,container_type,container_name,parameter_name,calculation_method,formula_rate,min_value,min_isallowed,max_value,max_isallowed,value_origin) VALUES(5015,'GENERAL','PROTEIN','Ontogeny factor GI table','ExpressionParameters','One_Rate',0.0,1,NULL,1,NULL);
+INSERT INTO tab_container_parameter_rates(container_id,container_type,container_name,parameter_name,calculation_method,formula_rate,min_value,min_isallowed,max_value,max_isallowed,value_origin) VALUES(5015,'GENERAL','PROTEIN','Ontogeny factor table','ExpressionParameters','One_Rate',0.0,1,NULL,1,NULL);
+UPDATE tab_container_parameter_rates SET formula_rate='TableFormulaWithXArgument_OntogenyFactor' WHERE container_id=5941 AND container_type='GENERAL' AND container_name='TRANSPORTER' AND parameter_name='Ontogeny factor' AND calculation_method='ExpressionParameters';
+UPDATE tab_container_parameter_rates SET formula_rate='TableFormulaWithXArgument_OntogenyFactorGI' WHERE container_id=5941 AND container_type='GENERAL' AND container_name='TRANSPORTER' AND parameter_name='Ontogeny factor GI' AND calculation_method='ExpressionParameters';
+INSERT INTO tab_container_parameter_rates(container_id,container_type,container_name,parameter_name,calculation_method,formula_rate,min_value,min_isallowed,max_value,max_isallowed,value_origin) VALUES(5941,'GENERAL','TRANSPORTER','Ontogeny factor GI table','ExpressionParameters','One_Rate',0.0,1,NULL,1,NULL);
+INSERT INTO tab_container_parameter_rates(container_id,container_type,container_name,parameter_name,calculation_method,formula_rate,min_value,min_isallowed,max_value,max_isallowed,value_origin) VALUES(5941,'GENERAL','TRANSPORTER','Ontogeny factor table','ExpressionParameters','One_Rate',0.0,1,NULL,1,NULL);
 INSERT INTO tab_container_parameter_rates(container_id,container_type,container_name,parameter_name,calculation_method,formula_rate,min_value,min_isallowed,max_value,max_isallowed,value_origin) VALUES(5958,'DISEASE_STATE','HI','Child-Pugh score','DiseaseStates','PARAM_ChildPughScore',0.0,1,2.0,1,NULL);
+INSERT INTO tab_container_parameters(container_id,container_type,container_name,parameter_name,can_be_varied,read_only,visible,can_be_varied_in_population,group_name,sequence,build_mode,building_block_type,is_input,is_changed_by_create_individual) VALUES(146,'ORGANISM','Organism','Post menstrual age',1,1,1,0,'BODY_ANATOMY',5,'LOCAL','INDIVIDUAL',0,1);
+INSERT INTO tab_container_parameters(container_id,container_type,container_name,parameter_name,can_be_varied,read_only,visible,can_be_varied_in_population,group_name,sequence,build_mode,building_block_type,is_input,is_changed_by_create_individual) VALUES(5015,'GENERAL','PROTEIN','Ontogeny factor GI table',1,0,1,0,'ONTOGENY_FACTOR',1,'GLOBAL','INDIVIDUAL',0,0);
+INSERT INTO tab_container_parameters(container_id,container_type,container_name,parameter_name,can_be_varied,read_only,visible,can_be_varied_in_population,group_name,sequence,build_mode,building_block_type,is_input,is_changed_by_create_individual) VALUES(5015,'GENERAL','PROTEIN','Ontogeny factor table',1,0,1,0,'ONTOGENY_FACTOR',1,'GLOBAL','INDIVIDUAL',0,0);
+INSERT INTO tab_container_parameters(container_id,container_type,container_name,parameter_name,can_be_varied,read_only,visible,can_be_varied_in_population,group_name,sequence,build_mode,building_block_type,is_input,is_changed_by_create_individual) VALUES(5941,'GENERAL','TRANSPORTER','Ontogeny factor GI table',1,0,1,0,'ONTOGENY_FACTOR',1,'GLOBAL','INDIVIDUAL',0,0);
+INSERT INTO tab_container_parameters(container_id,container_type,container_name,parameter_name,can_be_varied,read_only,visible,can_be_varied_in_population,group_name,sequence,build_mode,building_block_type,is_input,is_changed_by_create_individual) VALUES(5941,'GENERAL','TRANSPORTER','Ontogeny factor table',1,0,1,0,'ONTOGENY_FACTOR',1,'GLOBAL','INDIVIDUAL',0,0);
 INSERT INTO tab_container_parameters(container_id,container_type,container_name,parameter_name,can_be_varied,read_only,visible,can_be_varied_in_population,group_name,sequence,build_mode,building_block_type,is_input,is_changed_by_create_individual) VALUES(5958,'DISEASE_STATE','HI','Child-Pugh score',0,0,1,0,'DISEASE_STATES',1,'LOCAL','INDIVIDUAL',1,0);
 INSERT INTO tab_containers(container_id,container_type,container_name,parent_container_id,parent_container_type,parent_container_name,visible,is_logical) VALUES(5958,'DISEASE_STATE','HI',NULL,NULL,NULL,1,1);
 INSERT INTO tab_disease_states(disease_state,display_name,description) VALUES('HI','Hepatic Impairment Disease - (Edginton et al, 2008, Johnson et al, 2010)','Hepatic impairment is a multifactorial, progressive disease that is characterized by a loss of functional hepatocytes. Progression of disease may be classified by the Child-Pugh Score (A,B,C), which defines the level of disease severity and estimates prognosis. To apply this disease state to an individual in PK-Sim, first select the targeted Child-Pugh Score. This individual will display changes in blood flow to the portal vein, liver, kidney, heart, bone, fat, gonads, muscle, and skin. Additionally, changes in enzyme expression, plasma protein binding and hematocrit will be applied.  
@@ -9,14 +27,25 @@ This parameterization does not differentiate the etiology of hepatic impairment.
 INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Child-Pugh score','Child-Pugh score','Child-Pugh score: A (5,6 points)
 Child-Pugh score: B (7-9 points)
 Child-Pugh score: C (10-15 points) ',NULL,NULL);
+INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Ontogeny factor GI table','Ontogeny factor GI table','Ontogeny factor GI table','Dimensionless',NULL);
+INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Ontogeny factor table','Ontogeny factor table','Ontogeny factor table','Dimensionless',NULL);
+INSERT INTO tab_parameters(parameter_name,display_name,description,dimension,default_unit) VALUES('Post menstrual age','Post menstrual age','Post menstrual age','Age in years',NULL);
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('Asian_Tanaka_1996','HI');
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('BlackAmerican_NHANES_1997','HI');
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('European_ICRP_2002','HI');
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('Japanese_Population','CKD');
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('Japanese_Population','HI');
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('MexicanAmericanWhite_NHANES_1997','HI');
 INSERT INTO tab_population_disease_states(population,disease_state) VALUES('WhiteAmerican_NHANES_1997','HI');
+INSERT INTO tab_rate_container_parameters(calculation_method,formula_rate,container_id,container_type,container_name,parameter_name,alias) VALUES('ExpressionParameters','TableFormulaWithXArgument_OntogenyFactor',146,'ORGANISM','Organism','Post menstrual age','XArg');
+INSERT INTO tab_rate_container_parameters(calculation_method,formula_rate,container_id,container_type,container_name,parameter_name,alias) VALUES('ExpressionParameters','TableFormulaWithXArgument_OntogenyFactorGI',146,'ORGANISM','Organism','Post menstrual age','XArg');
+INSERT INTO tab_rate_generic_parameters(calculation_method,formula_rate,path_id,parameter_name,alias) VALUES('ExpressionParameters','TableFormulaWithXArgument_OntogenyFactor',240,'Ontogeny factor table','Table');
+INSERT INTO tab_rate_generic_parameters(calculation_method,formula_rate,path_id,parameter_name,alias) VALUES('ExpressionParameters','TableFormulaWithXArgument_OntogenyFactorGI',240,'Ontogeny factor GI table','Table');
+INSERT INTO tab_rate_generic_parameters(calculation_method,formula_rate,path_id,parameter_name,alias) VALUES('Individual_PKSim','PARAM_PostMenstrualAge',139,'Age','Age');
+INSERT INTO tab_rate_generic_parameters(calculation_method,formula_rate,path_id,parameter_name,alias) VALUES('Individual_PKSim','PARAM_PostMenstrualAge',139,'Gestational age','GA');
 INSERT INTO tab_rates(formula_rate,display_name,description) VALUES('PARAM_ChildPughScore','PARAM_ChildPughScore','PARAM_ChildPughScore');
+INSERT INTO tab_rates(formula_rate,display_name,description) VALUES('TableFormulaWithXArgument_OntogenyFactor','Ontogeny table formula','Ontogeny table formula');
+INSERT INTO tab_rates(formula_rate,display_name,description) VALUES('TableFormulaWithXArgument_OntogenyFactorGI','Ontogeny GI table formula','Ontogeny GI table formula');
 INSERT INTO tab_references(reference) VALUES('Edginton AN, Willmann S. Physiology-based simulations of a pathological condition: prediction of pharmacokinetics in patients with liver cirrhosis. Clin Pharmacokinet. 2008;47(11):743-52.');
 INSERT INTO tab_references(reference) VALUES('Johnson TN, Boussery K, Rowland-Yeo K, Tucker GT, Rostami-Hodjegan A. A semi-mechanistic model to predict the effects of liver cirrhosis on drug clearance. Clin Pharmacokinet. 2010;49(3):189-206.');
 INSERT INTO tab_value_origins(id,description,source,method) VALUES(93,'Edginton AN, Willmann S. Physiology-based simulations of a pathological condition: prediction of pharmacokinetics in patients with liver cirrhosis. Clin Pharmacokinet. 2008;47(11):743-52.','Publication','Undefined');