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Merge pull request #47 from OHDSI/ehr_Condition_Status_Concept_Id_doc…
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Update Optum_Panther_Diagnosis_STEM.md
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bradanton authored Jan 12, 2024
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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 | 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 | |
| primary_diagnosis | admitting_diagnosis | discharge_diagnosis | diagnosis_status | Set Condition_Status_Concept_Id to | comment |
| ----------------- | ------------------- | ------------------- | -------------------------------------------------------- | ---------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| 1 | 0 or NULL | 0 or NULL | any value except: 'History of', 'Possible diagnosis of' | 32902 | primary diagnosis |
| 1 | 1 | any value | any value except: 'History of', 'Possible diagnosis of' | 32901 | Primary admission diagnosis |
| 1 | 0 or NULL | 1 | any value except: 'History of', 'Possible diagnosis of' | 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 except: 'History of', 'Possible diagnosis of' | 32890 | Admission diagnosis |
| 0 or NULL | 0 or NULL | 1 | any value except: 'History of', 'Possible diagnosis of' | 32896 | Discharge diagnosis |
| else | | | | NULL | |


## Reading from OPTUM_EHR.Diagnosis
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