Generic-Condition-Drug-Topics-Notes
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Topic #TopicApproachPriorityDetailsActionContact
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Generic
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Low quality records, e.g. CPRD “researchable patient” flag
Kick out/create variable for CDM Work GroupHigh
Currently these records are kicked out or stored in "history of"
Determne few Use Cases for research

Update ETL document

Alignment with broader team and add guidelines to WIKI
James
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2Data inclusionCreate summary guideline, report % lossMedium
Add statistics about how much data inlcuded, how much was kicked out etc.. in ETL. Basically define and capture metadata about what assumptions were made, how much data made into CDM
Ex: populate metadata with 10% of observations landed in history
Reach out to Mui to understand existing metadata.
Guildlines for reporting %loss. How should we represent this? what is covered under Achilles.
Erica - scenarios of dropping a person from raw data
Erica will post the documentation on the forum
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3Start Date before Observation PeriodHistory of/First date of Observation PeriodHIGHBundle this into #1
Post the issue on forum and ask the community provide options
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4End Date - same day issueSpecial times (0.00 and 23.59)/BlankHIGHBundle this into #1
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5Socioeconomic, marital, language ConceptsCreate conventions for ConceptsMedium
Define and find a place to store these concepts.
List out concepts
Domain ID and mapping with fields. Clean up the existing domains
Reach out to Gowtham ( Bluecross..)
Asha
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6Flavors of 0Document
0s/unknowns/null/other/
for concept ids, foreign keys
Need a convention for id
- zeros
- null
Make a decision on making no nullable fields for IDs.
Document on WIKI
Erica to write recommendation
Process:
Sub group reivew of recommendation
Post on forum

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Source Value combo code+vocab ( non standard source value)
Concatenate/Leave blank and use Source Concept
MediumReach out to teams performing ETLsC
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8Source Value combo more than one
Concatenate/Leave blank and use Source Concept
C
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9Source Value combo code+name
Concatenate/Leave blank and use Source Concept
C
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10Source Concepts for local variables
Abolish SOURCE_TO_CONCEPT_MAP and
develop guidelines for creating Source Concepts >2B
EV
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11Source Concept=0 for Achillesmake not nullable for OMOP CDMC
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12Negative integersDevelop guidelineMedium
Ex: lab tests, units of injectables
Develop conventions for Measurments.
Make a decision on how to treat invalid #s & document
or leave up to analysts to treat invalid #s during analysis
Post multiple options( ETL changes) on the forum and collect feedback
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13Invalid numbersDevelop guidelinesMedium
Post multiple options( ETL changes) on the forum and collect feedback
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CONDITION
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14Concepts privacy issues
Data deleted for privacy in record/Mark deletions in
metadata/Establish Black List/Remove patients entirely/Set to 0
1. What are the rules for de-identification?
2. Recommendations for removing records or codes

Example: Major car accident, Sexual abuse concepts
Follow up wiht Mui for the entire list of privacy related concepts and post on forum
Post recommendation of removing records for the privacy related codes
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15Convert data from surveys?
Keep in Observation/Add, with explicit Type Concept.
Ex: do you have depression, Yes response to this question need to be mapped
C: Descritpion on this issue
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16Dedup?
Pick the highest Type Concept
Ex: Disagree on ICD level 1 on a claim, ICD level 2 on another claim, which one wins?
Erica: Recommend
option1 : dedup if mulitple concept ids recorded on the same day on in-patient claims
option 2: if multiple diagnosis recorded, pick the highest diagnosis
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17Clean up Type Concepts
Review the type concept list and clean up
Ex: inpatient/outpatient
Talk to Gowtham for claims
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18Derive pregnancies?Introduce
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19Visit_occurrence_id mandatory?
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20ICD Source value: With or without dotsIrrelevant with mandatory Source Concepts
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34Patient reported conditions
Table this topic for Day 2 of F2F workshop.
Need broader group for final recomendation
Erica - lead
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21DRUG
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22Duplicates for same dayDon't dedup
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End date guessing for prescribed, administered, mail-ordered
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24SigClean up and develop standard
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Contradiction between Sig, end date, days supply, amount
ETLer's problem
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26Dose Era logic
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27Patient reported drugs
Recommendations for patient reported conditions and drugs.
Ex: Reported in HRA forms, in hospitals
Janssen - stored in drug_exposure/cond occrance tables.
Type associated with patient reported drugs and conditions
Reccomendation: keep drugs in drug_exposure and record the type
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28Stop reasonConsider abolishing after polling
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Link between orders, administration, dispensing and filling
Publish guidelines
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30HCPCS and NDC on same lineConsider heuristic for picking
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31J code unitsConsider placing in quantity field
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32NDC9 to 11 mapping contradictionsConsider polling and vocab fix
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33NDC non-unique Concepts over timeCreate Black List
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35Drug_exposure_end_date for negative days_supply
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