Merge pull request #108 from OHDSI/ehr-add-microbiology

Add missed table

docs/OPTUM_PANTHER/Optum_Panther_Microbiology_STEM.md

@@ -0,0 +1,59 @@
+---
+layout: default
+title: Microbiology
+nav_order: 4
+parent: Optum EHR to STEM
+grand_parent: Optum EHR
+description: "OPTUM EHR Microbiology table to STEM"
+---
+
+# CDM Table name: STEM
+
+## Reading from OPTUM_EHR.Microbiology
+
+|     Destination Field    |     Source Field    |     Logic    |     Comment    |
+|-|-|-|-|
+| id | autogenerate  | | |
+| domain_id | Observation | | |
+| person_id | ptid | | |
+| visit_occurrence_id | encid | Lookup the VISIT_OCCURRENCE_ID based on the encid |If encid is blank then use coalesce(collect_date, result_date) to determine which VISIT_OCCURRENCE_ID the record should be associated to|
+| visit_detail_id| encid | Lookup the VISIT_DETAIL_ID based on the encid|If encid is blank then leave VISIT_DETAIL_ID blank|
+| provider_id |  encid | Lookup the PROVIDER_ID from the VISIT_DETAIL table using the encid|If encid is blank then leave PROVIDER_ID blank|
+| start_date | coalesce(collect_date, result_date)  | | |
+| end_date | coalesce(collect_date, result_date) | | | 
+| start_datetime | coalesce(collect_date, result_date) collect_time | Combine the coalesce(collect_date, result_date) and collect_time to create a datetime| |
+| end_datetime | coalesce(collect_date, result_date) collect_time | Combine the coalesce(collect_date, result_date) and collect_time to create a datetime| |
+| concept_id | 4252364 | Clinical microbiology | |
+|source_value|specimen_source|||
+| source_concept_id |0 || |
+| type_concept_id | 32835  | EHR Pathology report| | 
+| operator_concept_id |NULL | | |
+| unit_concept_id | | | |
+| unit_source_value | | | |
+| range_high | |  | | 
+| range_low |  | | |
+| value_as_number | | | |
+| value_as_string | organism |  | |
+| value_as_concept_id | | | |
+| value_source_value | organism | | |
+| verbatim_end_date |   | | |
+| days_supply |  | | |
+| dose_unit_source_value |  | | |
+| lot_number |  | | |
+| modifier_concept_id |   | | |
+| modifier_concept_id |  | | |
+| modifier_source_value |  | | |
+| quantity |  | | |
+| refills |  | | |
+| route_concept_id |  | | |
+| route_source_value |  | | |
+| sig |   | | |
+| stop_reason |  | | |
+| unique_device_id |  | | |
+| anatomic_site_concept_id |  | | |
+| disease_status_concept_id |   | | |
+| specimen_source_id | | | |
+| anatomic_site_source_value |  | | |
+| disease_status_source_value |  | | |
+| condition_status_concept_id | | | |
+| condition_status_source_value | | | |