Changes between Version 9 and Version 10 of Onyx to PDO

Timestamp:

01/10/12 22:41:28 (12 years ago)

Author:

jeff.lusted

Comment:

--

Onyx to PDO

@@ -32 +32 @@
 
 The '''__observation facts__''' holds one row for every fact (deemed sensible to include) that has been gleaned about a participant from the questionnaire.
+
+=== Building Observation Facts ===
+The strategy in dealing with Onyx variables is to fall back on accommodating them as either discrete variables (true/false) or enumerated variables. 
+In effect, not variables that can be measured by a continuous measure. This is in contrast to pathology tests, where the background is to expect a continuous measure of some sort.
+
+The following is the main algorithm for forming observation facts.
+
+For each variable relating to a participant...
+
+'''__Firstly__''', all of the following are ''''ignored'''':
+
+1. All variables from !QuestionnaireRun and !QuestionnaireMetric.
+2. All variables from Participant except for:
+   ethnicity, age, gender and recruitment type.
+3. Other primary diagnoses, other secondary diagnoses and other symptoms are textual note fields which should get folded into the associated 
+   "other" observation_fact. But I don't think they are. What should I do?
+4. Symptoms onset are ignored here and used instead as start date for the associated observation_fact.
+5. Patient email 1 and email 2 from the !EndContactQuestionnaire.
+6. !TubeCode, barcode and prefixCode from !UrineSamplesCollection and !BloodSamplesCollection.
+7. The following Onyx types: DATA, LOCALE and BINARY[[BR]]
+ 
+'''__Secondly__''', we examine the remainder for BOOLEANS where the answer is TRUE.[[BR]] 
+Some of these are (already) enumerated types (ie: not generated ones, but ones
+designed into the questionnaire itself), and are definite observation facts, 
+whilst others have an uncertain status. The only way to decide between the two 
+is to see whether we have ontological data within the refined metadata. If that exists, 
+then we are looking at an enumerated type and the value represents an observation fact. 
+These are processed as enumerations. The other BOOLEANS are reported upon.[[BR]][[BR]]
+                
+'''__Thirdly__''', non BOOLEANS where ontological data can be found are examined. [[BR]]
+It has to be said at the outset that each of these could be considered a discrete 
+observation fact, but as emphasized above, the overall strategy (at least as a point 
+of departure) has been to accommodate facts as either true/false statements or as 
+enumerations of values.
+
+This is what then happens:[[BR]]
+
+1. All variables where we have specifically designed for an enumeration are processed.
+   Currently, these are of type: 
+   
+   AGE, BEERNUMBER, BICEPS, CIGARETTENUMBER, CIGARNUMBER, DIASTOLICBP, ETHNICITY,
+   HEARTRATE, HEIGHT, HIPS, PIPENUMBER, RELATIVESNUMBER, SMALLNUMBER, SUBSCAPULAR,
+   SUPRAILIAC, SYSTOLICBP, TRICEPS, WAIST, WEIGHT, WINESPIRITNUMBER, YEAR, RECENTTIME.
+   
+   Note that these are types, and can therefore account for a considerable number of
+   facts (eg: YEAR covers every question where a year can be returned as an answer).
+   
+2. For type of DATETIME, if the variable concerns interventions this clinical episode,
+   then we build a non-generated enumeration using the datetime value as the 
+   observation start date. 
+   The other DATETIME variables are reported upon '''''but no facts built'''''. 
+   
+3. For types DECIMAL, INTEGER and TEXT 
+   variables are reported upon '''''but no facts built'''''.
+   
+4. For all others, variables are reported upon '''''but no facts built'''''.
+   
+'''__Fourthly__''', non BOOLEANS where ontological data cannot be found are examined.[[BR]]
+The following are special cases within this group where enumerations are built:
+
+1. Admin.Participant.age of type INTEGER          (generated enumeration)
+2. Admin.Participant.pat_ethnicity of type TEXT   (generated enumeration)
+3. Admin.Participant.gender of type TEXT          (built-in enumeration)
+4. Admin.Participant.recruitmentType of type TEXT (built-in enumeration)
+5. Admin.Participant.vital_status of type TEXT    (generated enumeration)
+
+Other variables within this group are reported upon '''''but no facts built'''''.[[BR]]
+
+'''__Lastly__''', any other variables are reported upon '''''but no facts built'''''.