added new ontologies to simulate bff/pxf

CNAG-Biomedical-Informatics · Feb 21, 2024 · b4fcce7 · b4fcce7
1 parent 94e3402
commit b4fcce7
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Showing 10 changed files with 146 additions and 75 deletions.
diff --git a/data/diseases_onts.yaml b/data/diseases_onts.yaml
diff --git a/data/phenos_onts.yaml b/data/phenos_onts.yaml
diff --git a/data/treatments_onts.yaml b/data/treatments_onts.yaml
diff --git a/data/weights_defaults.yaml b/data/weights_defaults.yaml
diff --git a/phenoRankeR/R/mod_sim_mode.R b/phenoRankeR/R/mod_sim_mode.R
@@ -107,6 +107,16 @@ mod_sim_mode_ui <- function(id){
                     height = "200px"
                   )
                 ),
+                tabPanel(
+                  title = "exposures",
+                  aceEditor(
+                    ns("yamlEditor_expos"),
+                    value = onts_defaults_phenos,
+                    mode = "yaml",
+                    theme = "github",
+                    height = "200px"
+                  )
+                ),
                 tabPanel(
                   title = "phenotypicFeatures",
                   aceEditor(
@@ -117,6 +127,16 @@ mod_sim_mode_ui <- function(id){
                     height = "200px"
                   )
                 ),
+                tabPanel(
+                  title = "procedures",
+                  aceEditor(
+                    ns("yamlEditor_procedures"),
+                    value = onts_defaults_procedures,
+                    mode = "yaml",
+                    theme = "github",
+                    height = "200px"
+                  )
+                ),
                 tabPanel(
                   title = "treatments",
                   aceEditor(
@@ -212,10 +232,29 @@ onts_defaults_treatments <- loadOntologyDefaults(
   "treatments"
 )
 
-writeYAMLDataToFile <- function(yaml_diseases, yaml_phenos, yaml_treatments) {
+onts_defaults_procedures <- loadOntologyDefaults(
+  "inst/extdata/defaults/procedures_onts.yaml",
+  "procedures"
+)
+
+onts_defaults_exposures <- loadOntologyDefaults(
+  "inst/extdata/defaults/exposures_onts.yaml",
+  "exposures"
+)
+
+writeYAMLDataToFile <- function(
+  yaml_diseases,
+  yaml_expos, 
+  yaml_phenos, 
+  yaml_procedures,
+  yaml_treatments
+  ) {
+
   yaml_data <- list()
   yaml_data$diseases <- yaml.load(yaml_diseases)
+  yaml_data$exposures <- yaml.load(yaml_expos)
   yaml_data$phenotypicFeatures <- yaml.load(yaml_phenos)
+  yaml_data$procedures <- yaml.load(yaml_procedures)
   yaml_data$treatments <- yaml.load(yaml_treatments)
 
   timestamp <- format(Sys.time(), "%Y%m%d%H%M%S")
@@ -245,19 +284,32 @@ simulate_data <- function(outputFormat, simulationId, simSettings) {
     ".json"
   )
 
+  print("simSettings")
+  print(simSettings)
+
   settings_diseases <- paste0(
     "-diseases ", simSettings[1],
     " -max-diseases-pool ", simSettings[2]
   )
 
+  settings_exposures <- paste0(
+    "-exposures ", simSettings[3],
+    " -max-exposures-pool ", simSettings[4]
+  )
+
   settings_phenos <- paste0(
-    "-phenotypicFeatures ", simSettings[3],
-    " -max-phenotypicFeatures-pool ", simSettings[4]
+    "-phenotypicFeatures ", simSettings[5],
+    " -max-phenotypicFeatures-pool ", simSettings[6]
+  )
+
+  settings_procedures <- paste0(
+    "-procedures ", simSettings[7],
+    " -max-procedures-pool ", simSettings[8]
   )
 
   settings_treatments <- paste0(
-    "-treatments ", simSettings[5],
-    " -max-treatments-pool ", simSettings[6]
+    "-treatments ", simSettings[9],
+    " -max-treatments-pool ", simSettings[10]
   )
 
   #normalizePath probably not needed
@@ -271,11 +323,15 @@ simulate_data <- function(outputFormat, simulationId, simSettings) {
     )),
     settings_diseases,
     " ",
+    settings_exposures,
+    " ",
     settings_phenos,
     " ",
+    settings_procedures,
+    " ",
     settings_treatments,
     " -n ",
-    simSettings[7],
+    simSettings[11],
     " -f ", outputFormat,
     " -o ", fn
   )
@@ -310,9 +366,15 @@ mod_sim_mode_server <- function(id, session, db_conn, db_driver, rv_sim){
     iv$enable()
 
     data <- data.frame(
-      ontologies = c("diseases", "phenotypicFeatures", "treatments"),
-      count = c(3, 3, 3),
-      max_pool_size = c(5, 5, 5)
+      ontologies = c(
+        "diseases",
+        "exposures",
+        "phenotypicFeatures",
+        "procedures",
+        "treatments"
+      ),
+      count = c(3, 3, 3, 3, 3),
+      max_pool_size = c(5, 5, 5, 5, 5)
     )
 
     # Render the DataTable with input fields for count and max_pool_size
@@ -367,6 +429,8 @@ mod_sim_mode_server <- function(id, session, db_conn, db_driver, rv_sim){
         updateAceEditor(session, "yamlEditor_diseases", value = "")
         updateAceEditor(session, "yamlEditor_phenos", value = "")
         updateAceEditor(session, "yamlEditor_treatments", value = "")
+        updateAceEditor(session, "yamlEditor_procedures", value = "")
+        updateAceEditor(session, "yamlEditor_expos", value = "")
         return()
       }
       output$errorOutput <- renderText(yamlValid)
@@ -390,12 +454,26 @@ mod_sim_mode_server <- function(id, session, db_conn, db_driver, rv_sim){
         "yamlEditor_treatments",
         value = as.yaml(yaml_data$treatments)
       )
+
+      updateAceEditor(
+        session,
+        "yamlEditor_procedures",
+        value = as.yaml(yaml_data$procedures)
+      )
+
+      updateAceEditor(
+        session,
+        "yamlEditor_expos",
+        value = as.yaml(yaml_data$exposures)
+      )
     })
 
     editors <- c(
       "yamlEditor_diseases",
       "yamlEditor_phenos",
-      "yamlEditor_treatments"
+      "yamlEditor_treatments",
+      "yamlEditor_procedures",
+      "yamlEditor_expos"
     )
 
     # TODO
@@ -425,7 +503,9 @@ mod_sim_mode_server <- function(id, session, db_conn, db_driver, rv_sim){
 
       simulationId <- writeYAMLDataToFile(
         input$yamlEditor_diseases,
+        input$yamlEditor_expos,
         input$yamlEditor_phenos,
+        input$yamlEditor_procedures,
         input$yamlEditor_treatments
       )
 

diff --git a/phenoRankeR/inst/extdata/defaults/diseases_onts.yaml b/phenoRankeR/inst/extdata/defaults/diseases_onts.yaml
@@ -1,11 +1,11 @@
 diseases:
-  - id: "HP:0000020"
-    label: "Urinary incontinence"
-  - id: "HP:0000055"
-    label: "Abnormality of female external genitalia"
-  - id: "HP:0000141"
-    label: "Amenorrhea"
-  - id: "HP:0000553"
-    label: "Abnormal uvea morphology"
-  - id: "HP:0000630"
-    label: "Abnormal retinal artery morphology"
+- id: OMIM:101000
+  label: Neurofibromatosis, type 2
+- id: OMIM:102578
+  label: Leukemia, acute promyelocytic, somatic
+- id: OMIM:103050
+  label: Adenylosuccinase deficiency
+- id: OMIM:103900
+  label: Aldosteronism, glucocorticoid-remediable
+- id: OMIM:104200
+  label: Alport syndrome, autosomal dominant
diff --git a/phenoRankeR/inst/extdata/defaults/exposures_onts.yaml b/phenoRankeR/inst/extdata/defaults/exposures_onts.yaml
@@ -0,0 +1,11 @@
+exposures:
+- id: NCIT:C194
+  label: 4-Nitroquinoline-1-Oxide
+- id: NCIT:C196
+  label: Benzo(a)pyrene-7,8-diol 9,10-Epoxide
+- id: NCIT:C197
+  label: Dimethylbenzanthracene
+- id: NCIT:C213
+  label: Aflatoxin
+- id: NCIT:C251
+  label: Anthracene
diff --git a/phenoRankeR/inst/extdata/defaults/phenos_onts.yaml b/phenoRankeR/inst/extdata/defaults/phenos_onts.yaml
@@ -1,11 +1,11 @@
 phenotypicFeatures:
-  - id: "OMIM:101000"
-    label: "Neurofibromatosis, type 2"
-  - id: "OMIM:102578"
-    label: "Leukemia, acute promyelocytic, somatic"
-  - id: "OMIM:103050"
-    label: "Adenylosuccinase deficiency"
-  - id: "OMIM:103900"
-    label: "Aldosteronism, glucocorticoid-remediable"
-  - id: "OMIM:104200"
-    label: "Alport syndrome, autosomal dominant"
+- id: HP:0000020
+  label: Urinary incontinence
+- id: HP:0000055
+  label: Abnormality of female external genitalia
+- id: HP:0000141
+  label: Amenorrhea
+- id: HP:0000553
+  label: Abnormal uvea morphology
+- id: HP:0000630
+  label: Abnormal retinal artery morphology
diff --git a/phenoRankeR/inst/extdata/defaults/procedures_onts.yaml b/phenoRankeR/inst/extdata/defaults/procedures_onts.yaml
@@ -0,0 +1,11 @@
+procedures:
+- id: NCIT:C1447
+  label: Barium Enema Injection
+- id: NCIT:C15189
+  label: Biopsy
+- id: NCIT:C15190
+  label: Needle Biopsy
+- id: NCIT:C15193
+  label: Bone Marrow Biopsy
+- id: NCIT:C15220
+  label: Diagnosis
diff --git a/phenoRankeR/inst/extdata/defaults/treatments_onts.yaml b/phenoRankeR/inst/extdata/defaults/treatments_onts.yaml
@@ -1,11 +1,15 @@
 treatments:
-  - id: "RxNorm:1000000"
-    label: "amlodipine 5 MG / hydrochlorothiazide 12.5 MG / olmesartan medoxomil 40 MG Oral Tablet [Tribenzor]"
-  - id: "RxNorm:1000001"
-    label: "amlodipine 5 MG / hydrochlorothiazide 25 MG / olmesartan medoxomil 40 MG Oral Tablet"
-  - id: "RxNorm:1000005"
-    label: "amlodipine 5 MG / hydrochlorothiazide 25 MG / olmesartan medoxomil 40 MG Oral Tablet [Tribenzor]"
-  - id: "RxNorm:1000009"
-    label: "dimethicone 100 MG/ML / miconazole nitrate 20 MG/ML / zinc oxide 100 MG/ML Topical Spray"
-  - id: "RxNorm:1000048"
-    label: "doxepin 10 MG Oral Capsule"
+- id: RxNorm:1000000
+  label: amlodipine 5 MG / hydrochlorothiazide 12.5 MG / olmesartan medoxomil 40 MG
+    Oral Tablet [Tribenzor]
+- id: RxNorm:1000001
+  label: amlodipine 5 MG / hydrochlorothiazide 25 MG / olmesartan medoxomil 40 MG
+    Oral Tablet
+- id: RxNorm:1000005
+  label: amlodipine 5 MG / hydrochlorothiazide 25 MG / olmesartan medoxomil 40 MG
+    Oral Tablet [Tribenzor]
+- id: RxNorm:1000009
+  label: dimethicone 100 MG/ML / miconazole nitrate 20 MG/ML / zinc oxide 100 MG/ML
+    Topical Spray
+- id: RxNorm:1000048
+  label: doxepin 10 MG Oral Capsule