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Merge pull request #45 from OHDSI/ehr_doc_upd
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latest (Dec-2023) ehr changes were added to documentation
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@bradanton
bradanton authored Dec 21, 2023
2 parents 4de3ca1 + 5612d0b commit 7ebc355
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36 changes: 36 additions & 0 deletions docs/OPTUM_PANTHER/Optum_Panther_Device_Exposure.md
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---
layout: default
title: Optum EHR Device Exposure
nav_order: 9
parent: Optum EHR
description: "Device Exposure Quantity Imputation"

---

# Optum EHR Device Quantity Imputation

## Table name: device_exposure


| Destination Field | Source field | Logic | Comment field |
| --- | --- | --- | --- |
| device_exposure_id | id | | |
| person_id | person_id | | |
| device_concept_id | concept_id | | |
| device_exposure_start_date | start_date | | |
| device_exposure_start_datetime | start_datetime | | |
| device_exposure_end_date | end_date | | |
| device_exposure_end_datetime | end_datetime | | |
| device_type_concept_id | type_concept_id | | |
| unique_device_id | unique_device_id | | |
| quantity | quantity | set QUANTITY = NULL where DEVICE_EXPOSURE.quantity <1 | |
| provider_id | provider_id | | |
| visit_occurrence_id | visit_occurrence_id | | |
| visit_detail_id | | | |
| device_source_value | source_value | | |
| device_source_concept_id | source_concept_id | | |

### Change log

- 12-Dec-2023
Added quantity logic
25 changes: 14 additions & 11 deletions docs/OPTUM_PANTHER/Optum_Panther_Diagnosis_STEM.md
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Expand Up @@ -11,16 +11,16 @@ description: "OPTUM EHR Diagnosis table to STEM"

The **Diagnosis** table has multiple columns we use to assign CONDITION_STATUS_CONCEPT_ID. These are PRIMARY_DIAGNOSIS, ADMITTING_DIAGNOSIS, DISCHARGE_DIAGNOSIS, and DISCHARGE_STATUS. The below table details the possible combinations of the fields and how to assign the CONDITION_STATUS_CONCEPT_ID accordingly.

|Primary_Diagnosis Value| Admitting_Diagnosis Value |Discharge_Diagnosis Value| Discharge_Status Value| **Set Condition_Status_Concept_Id to**|
|-|-|-|-|-|
|1| 0 |0 |any value |32902|
1| 1 |any value| any value |32901|
1| 0 |1 |any value| 32903|
0 |0 |0| History of| 4188893|
0| 0 |0| Possible diagnosis of| 32899|
0|1|any value|any value|32830|
0|0|1|any value|32896|
0|0|0|any value | 0
| primary_diagnosis | admitting_diagnosis | discharge_diagnosis | diagnosis_status | Set Condition_Status_Concept_Id to | comment |
| ----------------- | ------------------- | ------------------- | --------------------- | ---------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| 1 | 0 or NULL | 0 or NULL | any value | 32902 | primary diagnosis |
| 1 | 1 | any value | any value | 32901 | Primary admission diagnosis |
| 1 | 0 or NULL | 1 | any value | 32903 | Primary discharge diagnosis |
| any value | any value | any value | History of | | put it in the Observation table with observation_concept_id = 1340204 and value_as_concept_id = mapped diagnosis_cd_type&diagnosis_cd (same logic as described in concept_Id). Note, if the source concept is mapped with Maps to value, ignore this relationship. type_concept_id = 32840, source_value = 'History of '||diagnosis_cd,  other fields have the same logic as described in Reading from OPTUM_EHR.Diagnosis |
| any value | any value | any value | Possible diagnosis of | 32899 | Preliminary diagnosis |
| 0 or NULL | 1 | any value | any value | 32890 | Admission diagnosis |
| 0 or NULL | 0 or NULL | 1 | any value | 32896 | Discharge diagnosis |
| else | | | | NULL | |


## Reading from OPTUM_EHR.Diagnosis
Expand Down Expand Up @@ -83,4 +83,7 @@ The **Diagnosis** table has multiple columns we use to assign CONDITION_STATUS_C
- Updates condition_status accordingly so diagnosi_status is concatenated along with poa, admitting_diagnosis, discharge_diagnosis, and primary_diagnosis

### 01-Aug-2023
- Added Maps to value logic
- Added Maps to value logic

### 12-Dec-2023
CONDITION_STATUS_CONCEPT_ID logic updated
9 changes: 7 additions & 2 deletions docs/OPTUM_PANTHER/Optum_Panther_Drug_Exposure.md
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Expand Up @@ -34,7 +34,7 @@ We apply this imputation strategy after data has been moved to the DRUG_EXPOSURE
| drug_type_concept_id | type_concept_id | | |
| stop_reason | stop_reason | | |
| refills | refills | | |
| quantity | quantity | | |
| quantity | quantity | Allowed number of refills up to 24. if this number is higher, set drug_expusure.refills = NULL | |
| days_supply | days_supply | | |
| sig | sig | | |
| route_concept_id | route_concept_id | | |
Expand All @@ -45,4 +45,9 @@ We apply this imputation strategy after data has been moved to the DRUG_EXPOSURE
| drug_source_value | source_value | | |
| drug_source_concept_id | source_concept_id | | |
| route_source_value | route_source_value | | |
| dose_unit_source_value | dose_unit_source_value | | |
| dose_unit_source_value | dose_unit_source_value | | |

### Change log

- 12-Dec-2023
Set max allowed refills up to 24
2 changes: 1 addition & 1 deletion docs/OPTUM_PANTHER/Optum_Panther_Note_NLP.md
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---
layout: default
title: Optum EHR to Note_NLP
nav_order: 8
nav_order: 10
parent: Optum EHR
has_children: false
description: "Note NLP table description"
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7 changes: 5 additions & 2 deletions docs/OPTUM_PANTHER/Optum_Panther_STEM.md
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Expand Up @@ -16,7 +16,7 @@ This logic is reiterated from the PERSON table page but is put here as well for
The Optum EHR Patient table contains an indicator that denotes whether the paient is part of an integrated delivery network, which means that there is a higher likelihood of complete capture of medical events. An integrated delivery network is an organization or group of hospitals and health care providers that aligns local facilities, managing them as one. To keep track of this, for each person in the Patient table with **idn_indicator** = 1, create a record in the OBSERVATION table where OBSERVATION_DATE = OBSERVATION_PERIOD_START_DATE, OBSERVATION_CONCEPT_ID = 44804235 and VALUE_AS_NUMBER = 1, OBSERVATION_SOURCE_VALUE = 'IDN' and OBSERVATION_TYPE_CONCEPT_ID = 32817 (EHR).

Dataset contains dates beore 2007 year, which are mistakes, since the start of the dataset is 01-Jan-2007. Events with these dates are removed from the CDM.

Additionally needs to be removed any events that has an event date year that is prior to the person YEAR_OF_BIRTH.

**Fields in the STEM table**

Expand Down Expand Up @@ -70,4 +70,7 @@ Dataset contains dates beore 2007 year, which are mistakes, since the start of t
### Change log

- 07-Aug-2023
Cut of dates before 01-Jan-2007 rule added
Cut of dates before 01-Jan-2007 rule added

- 12-Dec-2023
Delete events with year prior to the person YEAR_OF_BIRTH
2 changes: 1 addition & 1 deletion docs/OPTUM_PANTHER/oncology module - all logic.md
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---
layout: default
title: Oncology module ETL
nav_order: 10
nav_order: 11
parent: Optum EHR
description: "Oncology Module ETL documentation"

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