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output_description.txt
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The output description:
Writes an Excel file to disk.
definitions used:
"Node concept" is a concept directly used in Concept Set Expression
"includedescendants": indicates whether descendants of "Node concept" are included in concept set, 0 stands for False, 1 stands for True
"isexcluded": indicates whether "Node concept" and it's descendants if "includedescendants" = 1 are excluded from a concept set, 0 stands for False, 1 stands for True
"drc": descendant record count - summary number of
"source concept": the concept set definition is usualy done through standard concepts.
Different clinical events might be captured with the same set of included standard concepts if mapping was changed, that's why the tool tracks source concepts related.
The Excel file has the following tabs:
1. summaryTable
sum of added or removed source concepts occurrences in a dataset
- for example, the cohort_id 123 doesn't pick up source codes X and Y when using newer vocabulary version. X appears 10 times in the data, Y appears 15 times.
In this situation you'll get the following output:
cohortid | action | sum
123 | Removed| 25
2. nonStNodes
lists non-standard concepts used in the concept set definition.
Note, the concept set definition JSON isn't updated with the vocabulary updates, so you will not see concept changes in Atlas.
So you need to run this tool to see non-stanard concepts (added by mistake or become non-standard over time)
For example, the cohort_id 123 has conceptset ='depressoin' which has Node concept = "4059192|History of depression" with descendants included,
this concept is non-standard and mapped this way:
Maps to "1340204|History of event"
Maps to value "440383|Depressive disorder"
In this situation you'll get the following output:
cohortid | conceptsetname | conceptsetid | isexcluded | includedescendants | nodeConceptId | nodeConceptName | drc | mapsToConceptId | mapsToConceptName | mapsToValueConceptId | mapsToValueConceptName
123 | depressoin | 1 | 0 | 1 | 4059192 | History of depression | 45678 | 1340204 | History of event | 440383 |Depressive disorder
3. mapDif
Shows related source concepts that were added or removed with their mapping for reference.
This way user knows why the difference in related source concepts occurrs.
For example,
- first part is common for 3 checks, explain it in the begeninning
cohortdefinitionid 3466
cohortname [PL] Earliest event of Systemic lupus erythematosus
conceptsetname SLE plus signs and symptoms of SLE
node_concept_id 77074
node_concept_name Joint pain
isexcluded 0
includedescendants 0
action Added
sourceconceptid 44831507
sourceconceptname Pain in joint, lower leg
sourceconceptcode 719.46
sourcevocabularyid ICD9CM
NewMappedConceptid 77074
NewMappedconceptname Joint pain
oldmappedconceptid 4150062
oldmappedconceptname Knee pain
Totalcount* 132464334
4.peakDif
"Peak concept": the common parent concept of added or removed standard concepts above which the hierarchy is changed
cohortid conceptsetid conceptsetname isexcluded includedescendants nodeConceptId nodeConceptName action peakConceptId peakName peakCode drc
cohortid 12825
conceptsetid 23
conceptsetname Headache
isexcluded 0
includedescendants 1
nodeConceptId 378253
nodeConceptName Headache
action Added
peakConceptId 375527
peakName Headache disorder
peakCode 230461009
drc 34219562