Updated queries/subqueries

neuml · Jun 16, 2020 · 0e47b3b · 0e47b3b
1 parent d97f0a9
commit 0e47b3b
Show file tree

Hide file tree

Showing 4 changed files with 75 additions and 39 deletions.
diff --git a/tasks/factors.yml b/tasks/factors.yml
@@ -14,13 +14,13 @@ fields:
         - {name: Factors, query: $QUERY, question: what containment method}
         - {name: Influential, constant: "-"}
         - {name: Excerpt, query: $QUERY, question: what containment method, snippet: true}
-        - {name: Measure of Evidence, constant: "-"}
+        - {name: Measure of Evidence, query: countries cities, question: What locations}
 
     weather: &weather
         - {name: Factors, query: temperature humidity, question: What weather factor}
         - {name: Influential, constant: "-"}
         - {name: Excerpt, query: temperature humidity, question: How weather effects virus}
-        - {name: Measure of Evidence, constant: "-"}
+        - {name: Measure of Evidence, query: countries cities, question: What locations}
 
     appendix: &appendix
         - name: Sample Size
@@ -66,7 +66,7 @@ Evidence that domesticated_farm animals can be infected and maintain transmissib
         - {name: Factors, query: animals studied, question: what animals}
         - {name: Influential, constant: "-"}
         - {name: Excerpt, query: animals studied, question: "Can animals transmit SARS-COV-2"}
-        - {name: Measure of Evidence, constant: "-"}
+        - {name: Measure of Evidence, query: confirmation method, question: What rna confirmation method used}
         - *appendix
 
 How does temperature and humidity affect the transmission of 2019-nCoV_:

diff --git a/tasks/models.yml b/tasks/models.yml
@@ -10,6 +10,11 @@ fields:
         - name: Journal
         - name: Study Type
 
+    methods: &methods
+        - {name: Method, query: confirmation method, question: What rna confirmation method used}
+        - {name: Result, query: $QUERY conclusions findings results, question: What is conclusion on $QUERY}
+        - {name: Measure of Evidence, constant: "-"}
+
     appendix: &appendix
         - name: Sample Size
         - name: Sample Text
@@ -21,6 +26,7 @@ Are there studies about phenotypic change_:
     query: Phenotypic genetic change
     columns:
         - *common
+        - *methods
         - *appendix
 
 Efforts to develop qualitative assessment frameworks:
@@ -37,18 +43,23 @@ How can we measure changes in COVID-19_s behavior in a human host as the virus e
     query: Human immune response to COVID-19
     columns:
         - *common
+        - *methods
         - *appendix
 
 Serial Interval (time between symptom onset in infector-infectee pair):
     query: Serial Interval (for infector-infectee pair)
     columns:
         - *common
+        - {name: Age, query: median patient age, question: What is median patient age}
+        - {name: Sample Obtained, query: throat respiratory fecal sample, question: What sample}
+        - {name: Serial Interval (days), query: serial interval days, question: What is median serial interval}
         - *appendix
 
 Studies to monitor potential adaptations:
     query: studies monitor adaptations
     columns:
         - *common
+        - *methods
         - *appendix
 
 What do models for transmission predict_:
@@ -63,10 +74,12 @@ What is known about adaptations (mutations) of the virus_:
     query: Virus mutations
     columns:
         - *common
+        - *methods
         - *appendix
 
 What regional genetic variations (mutations) exist:
     query: Regional genetic variations (mutations)
     columns:
         - *common
+        - *methods
         - *appendix
diff --git a/tasks/patients.yml b/tasks/patients.yml
@@ -12,10 +12,15 @@ fields:
 
     asymptomatic: &asymptomatic
         - {name: Age, query: median patient age, question: What is median patient age}
-        - {name: Sample Obtained, constant: "-"}
+        - {name: Sample Obtained, query: throat respiratory fecal sample, question: What sample}
         - {name: Asymptomatic Transmission, query: proportion percent asymptomatic patients, question: What percent asymptomatic}
         - {name: Excerpt, query: proportion percent asymptomatic patients, question: What percent asymptomatic, snippet: true}
 
+    incubation: &incubation
+        - {name: Age, query: median patient age, question: What is median patient age}
+        - {name: Days, query: range of incubation period days, question: What is median incubation period}
+        - {name: Range (Days), query: range of incubation periods days, question: What is incubation period range}
+
     appendix: &appendix
         - name: Sample Size
         - name: Sample Text
@@ -31,33 +36,37 @@ Can the virus be transmitted asymptomatically or during the incubation period_:
         - *appendix
 
 How does viral load relate to disease presentations and likelihood of a positive diagnostic test_:
-    query: Advances in diagnosing SARS-COV-2 detection methods
+    query: viral load relation to positive diagnostic test
     columns:
         - *common
+        - {name: Age, query: median patient age, question: What is median patient age}
+        - {name: Sample Obtained, query: throat respiratory fecal sample, question: What sample}
+        - {name: Excerpt, query: $QUERY, question: What is $QUERY, snippet: True}
         - *appendix
 
 Incubation period across different age groups:
     query: Incubation period children adult elderly days
     columns:
         - *common
-        - {name: Age, query: median patient age, question: What is median patient age}
-        - {name: Days, query: range of incubation period days, question: What is median incubation period}
-        - {name: Range (Days), query: range of incubation periods days, question: What is incubation period range}
+        - *incubation
         - *appendix
 
 Length of viral shedding after illness onset:
     query: Shedding duration days
     columns:
         - *common
-        - {name: Age, query: median patient age, question: What is median patient age}
-        - {name: Days, query: range of incubation period days, question: What is median incubation period}
-        - {name: Range (Days), query: range of incubation periods days, question: What is incubation period range}
+        - *incubation
         - *appendix
 
 Manifestations of COVID-19 including but not limited to possible cardiomyopathy and cardiac arrest:
-    query: Cardiomyopathy and cardiac arrest related manifestations
+    query: virus related manifestations
     columns:
         - *common
+        - {name: Age, query: median patient age, question: What is median patient age}
+        - {name: Sample Obtained, query: throat respiratory fecal sample, question: What sample}
+        - {name: Manifestation, query: clinical manifestations, question: What manifestations}
+        - {name: Frequency of Symptoms, query: symptoms frequency, question: What was frequency of symptoms}
+        - {name: Excerpt, query: clinical manifestations, question: What manifestations, snippet: True}
         - *appendix
 
 Proportion of all positive COVID19 patients who were asymptomatic:
@@ -78,7 +87,5 @@ What is the incubation period of the virus_:
     query: Range of incubation periods days
     columns:
         - *common
-        - {name: Age, query: median patient age, question: What is median patient age}
-        - {name: Days, query: range of incubation period days, question: What is median incubation period}
-        - {name: Range (Days), query: range of incubation periods days, question: What is incubation period range}
+        - *incubation
         - *appendix
diff --git a/tasks/risks.yml b/tasks/risks.yml
@@ -29,97 +29,113 @@ fields:
         - *appendix
 
 Age:
-    query: Age CI
+    query: +age ci
     columns: *columns
 
 Asthma:
-    query: Asthma CI
+    query: +asthma ci
+    columns: *columns
+
+Autoimmune disorders:
+    query: +autoimmune disorders ci
     columns: *columns
 
 Cancer:
-    query: Cancer CI
+    query: +cancer ci
     columns: *columns
 
 Cardio- and cerebrovascular disease:
-    query: Cardio and Cerebrovascular disease CI
+    query: cardio and +cerebrovascular disease ci
     columns: *columns
 
 Cerebrovascular disease:
-    query: Cerebrovascular disease CI
+    query: +cerebrovascular disease ci
     columns: *columns
 
 Chronic digestive disorders:
-    query: Digestive disorders CI
+    query: +digestive disorders ci
     columns: *columns
 
 Chronic kidney disease:
-    query: Kidney disease CKD CI
+    query: +kidney disease ckd ci
     columns: *columns
 
 Chronic liver disease:
-    query: Liver disease CI
+    query: +liver disease ci
     columns: *columns
 
 Chronic respiratory diseases:
-    query: Chronic respiratory disease CI
+    query: chronic +respiratory disease ci
     columns: *columns
 
 COPD:
-    query: Chronic obstructive pulmonary disease COPD CI
+    query: chronic obstructive pulmonary disease +copd ci
     columns: *columns
 
 Dementia:
-    query: Dementia CI
+    query: +dementia ci
     columns: *columns
 
 Diabetes:
-    query: Diabetes CI
+    query: +diabetes ci
     columns: *columns
 
 Drinking:
-    query: Alcohol Abuse CI
+    query: +alcohol abuse ci
     columns: *columns
 
 Endocrine diseases:
-    query: Endocrine disease CI
+    query: +endocrine disease ci
     columns: *columns
 
 Ethnicity_ Hispanic vs. non-Hispanic:
-    query: Hispanic race CI
+    query: +hispanic race ci
     columns: *columns
 
 Heart Disease:
-    query: Heart Disease CI
+    query: +heart +disease ci
     columns: *columns
 
 Heart Failure:
-    query: Heart Failure CI
+    query: +heart +failure ci
     columns: *columns
 
 Hypertension:
-    query: Hypertension CI
+    query: +hypertension ci
     columns: *columns
 
 Immune system disorders:
-    query: Immune system disorder CI
+    query: +immune system disorder ci
     columns: *columns
 
 Male gender:
-    query: Male CI
+    query: +male ci
+    columns: *columns
+
+Neurological disorders:
+    query: +neurological disorders ci
     columns: *columns
 
 Overweight or obese:
-    query: Overweight obese CI
+    query: +overweight obese ci
+    columns: *columns
+
+Race_ Asian vs. White:
+    query: race +asian +white ci
     columns: *columns
 
 Race_ Black vs. White:
-    query: Race black white CI
+    query: race +black +white ci
+    columns: *columns
+
+Race_ Other vs. White:
+    query: race +white ci
     columns: *columns
 
 Respiratory system diseases:
-    query: Respiratory disease CI
+    query: +respiratory disease ci
     columns: *columns
 
 Smoking Status:
-    query: Smoking smoker ci
+    query: +smoking smoker ci
     columns: *columns