From 2d49923a2784174a1cdb7ae6324f6f71e7bb476d Mon Sep 17 00:00:00 2001 From: sgasmanjj Date: Fri, 27 Sep 2024 16:09:18 -0400 Subject: [PATCH 1/6] Admitting source value addition Add G as an admitting source value mapping to "Other place of service" --- docs/PREMIER/Premier_Visit_Occurrence.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/PREMIER/Premier_Visit_Occurrence.md b/docs/PREMIER/Premier_Visit_Occurrence.md index fd41a610..a6f32957 100644 --- a/docs/PREMIER/Premier_Visit_Occurrence.md +++ b/docs/PREMIER/Premier_Visit_Occurrence.md @@ -28,7 +28,7 @@ Admitting and discharge information is captured in Premier as the place of servi |CARE_SITE_ID|PAT.PROV_ID||| |VISIT_SOURCE_VALUE|PAT.I_O_IND||| |VISIT_SOURCE_CONCEPT_ID|-||| -|ADMITTING_SOURCE_CONCEPT_ID|PAT.POINT_OF_ORIGIN|if POINT_OF_ORIGIN then ADMITTING_SOURCE_CONCEPT_ID
0 then 8976
1 then 8844
2 then 8716
3 then 8844
4 then 8717
45 then 581384
46 then 8650
5 then 8863
6 then 8844
7 then 8870
8 then 8844
9 then 8844
A then 8761
B then 8536
C then 8536
D then 8717
E then 8883
F then 8546
|| +|ADMITTING_SOURCE_CONCEPT_ID|PAT.POINT_OF_ORIGIN|if POINT_OF_ORIGIN then ADMITTING_SOURCE_CONCEPT_ID
0 then 8976
1 then 8844
2 then 8716
3 then 8844
4 then 8717
45 then 581384
46 then 8650
5 then 8863
6 then 8844
7 then 8870
8 then 8844
9 then 8844
A then 8761
B then 8536
C then 8536
D then 8717
E then 8883
F then 8546
G then 8844
|| |ADMITTING_SOURCE_VALUE|PAT. POINT_OF_ORIGIN|PAT. POINT_OF_ORIGIN|| |DISCHARGE_TO_CONCEPT_ID|PAT.DISC_STATUS|If DISC_STATUS then DISCHARGE_TO_CONCEPT_ID
1 then 8536, 2 then 8844
3 then 8863, 4 then 8863
5 then 8844, 6 then 8536
7 then 8844, 8 then 8536
9 then 8717, 20 then NULL
21 then 8844, 30 then 8844
40 then 8546, 41 then 8546
42 then 8546, 43 then 8966
50 then 8546, 51 then 8546
61 then 8863, 62 then 8920
63 then 8970, 64 then 8676
65 then 8971, 66 then 581379
69 then 8844, 70 then 8844
71 then 8844, 72 then 8717
81 then 8536, 82 then 581379
83 then 8863, 84 then 8827
85 then 8844, 86 then 8536
87 then 8844, 88 then 8966
89 then 8863, 90 then 581379
91 then 581379, 92 then 8676
93 then 8971, 94 then 581379
95 then 8844, 99 then 8844
|| |DISCHARGE_TO_SOURCE_VALUE|PAT.DISC_STATUS|PAT.DISC_STATUS|| From 48edbeb395b0e740ae3773b7eedd630a1e06671e Mon Sep 17 00:00:00 2001 From: sgasmanjj Date: Fri, 27 Sep 2024 16:17:18 -0400 Subject: [PATCH 2/6] Update observation documentation Update observation documentation to reflect removal of admission and discharge information --- docs/PREMIER/Premier_Observation.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/PREMIER/Premier_Observation.md b/docs/PREMIER/Premier_Observation.md index d4a51154..1c5c92d9 100644 --- a/docs/PREMIER/Premier_Observation.md +++ b/docs/PREMIER/Premier_Observation.md @@ -8,7 +8,7 @@ layout: default # Table Name: Observation -The observation table houses additional demographic and visit data that is housed in Premier. Certain ICD9, CPT, and standard charge codes map to standardized observation table concept. Marital status, admission information, discharge status, and patient type records are specific to Premier and map to non-standard observation table concepts. +The observation table houses additional demographic and visit data that is housed in Premier. Certain ICD9, CPT, and standard charge codes map to standardized observation table concept. Marital status and patient type records are specific to Premier and map to non-standard observation table concepts. Additionally, procedures that occur on the same day as billing records for operation time will have operation time calculated and recorded in the observation table. @@ -53,4 +53,4 @@ The field mapping is performed as follows: ### 01-Aug-2023 - Added Maps to value logic -- Cleared formatting \ No newline at end of file +- Cleared formatting From 695f12688220a59150b5460efdcdf50c73550067 Mon Sep 17 00:00:00 2001 From: sgasmanjj Date: Fri, 27 Sep 2024 16:23:51 -0400 Subject: [PATCH 3/6] Update Premier_Observation.md --- docs/PREMIER/Premier_Observation.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/PREMIER/Premier_Observation.md b/docs/PREMIER/Premier_Observation.md index 1c5c92d9..8ae65672 100644 --- a/docs/PREMIER/Premier_Observation.md +++ b/docs/PREMIER/Premier_Observation.md @@ -14,7 +14,7 @@ Additionally, procedures that occur on the same day as billing records for opera PATICD_DIAG.ICD_CODE, PATICD_PROC.ICD_CODE, PATCPT.CPT_CODE, and PATBILL.STD_CHG_CODE map to OBSERVATION.OBSERVATION_CONCEPT_ID using the source to standard cte_vocab_map. These records also map to OBSERVATION.OBSERVATION_SOURCE_CONCEPT_ID using the source to source cte_vocab_map. -PAT.MART_STATUS, PAT.POINT_OF_ORIGIN, PAT.DISC_STATUS, and PAT.PATTYPE map to set OBSERVATION_CONCEPT_ID codes described in the table below and OBSERVATION_SOURCE_CONCEPT_ID=0. +PAT.MART_STATUS and PAT.PATTYPE map to set OBSERVATION_CONCEPT_ID codes described in the table below and OBSERVATION_SOURCE_CONCEPT_ID=0. The observation start date is assigned the VISIT_START_DATE. The ASSOCIATED_PROVIDER_ID that is provided is the randomly generated key provided by Premier for the provider that admitted the patient. There are two providers that exist in Premier, the admitting and attending. This ETL makes the decision to use admitting because it is unknown whether the admitting provider, attending provider or another person diagnosed the person. @@ -32,12 +32,12 @@ The field mapping is performed as follows: |--- |--- |--- |--- | |OBSERVATION_ID|-|System-generated|| |PERSON_ID|PAT.MEDREC_KEY||| -|OBSERVATION_CONCEPT_ID|PATCPT.CPT_COD
PATBILL.STD_CHG_CODE
PATICD_PROC.ICD_CODEPAT
ICD_DIAG.ICD_CODE|For records from PATCPT.CPT_CODE, and PATBILL.STD_CHG_CODE:

QUERY: SOURCE TO STANDARD SELECT TARGET_CONCEPT_ID FROM CTE_VOCAB_MAP WHERE SOURCE_VOCABULARY_ID IN ('CPT4', 'HCPCS', 'JNJ_PMR_OBS_CODE', 'JNJ_PMR_PROC_CHRG_CD') AND TARGET_DOMAIN_ID = 'Observation'

For records from PATICD_PROC.ICD_CODE and PATICD_DIAG.ICD_CODE: where ICD_VERSION=9 QUERY: SOURCE TO STANDARD SELECT TARGET_CONCEPT_ID FROM CTE_VOCAB_MAP WHERE SOURCE_VOCABULARY_ID IN ('ICD9CM') AND TARGET_DOMAIN_ID = 'Observation'

For records from PATICD_PROC.ICD_CODE and PATICD_DIAG.ICD_CODE:where ICD_VERSION=10 QUERY: SOURCE TO STANDARD SELECT TARGET_CONCEPT_ID FROM CTE_VOCAB_MAP WHERE SOURCE_VOCABULARY_ID IN ('ICD10CM') AND TARGET_DOMAIN_ID = 'Observation'

For PAT.MART_STATUS, OBSERVATION_CONCEPT_ID=4053609

For PAT.POINT_OF_ORIGIN, OBSERVATION_CONCEPT_ID=40757183

For PAT.DISC_STATUS, OBSERVATION_CONCEPT_ID=40757177

For PAT.PATTYPE, OBSERVATION_CONCEPT_ID=40769091

When operation time observation values then 3016562|| +|OBSERVATION_CONCEPT_ID|PATCPT.CPT_COD
PATBILL.STD_CHG_CODE
PATICD_PROC.ICD_CODEPAT
ICD_DIAG.ICD_CODE|For records from PATCPT.CPT_CODE, and PATBILL.STD_CHG_CODE:

QUERY: SOURCE TO STANDARD SELECT TARGET_CONCEPT_ID FROM CTE_VOCAB_MAP WHERE SOURCE_VOCABULARY_ID IN ('CPT4', 'HCPCS', 'JNJ_PMR_OBS_CODE', 'JNJ_PMR_PROC_CHRG_CD') AND TARGET_DOMAIN_ID = 'Observation'

For records from PATICD_PROC.ICD_CODE and PATICD_DIAG.ICD_CODE: where ICD_VERSION=9 QUERY: SOURCE TO STANDARD SELECT TARGET_CONCEPT_ID FROM CTE_VOCAB_MAP WHERE SOURCE_VOCABULARY_ID IN ('ICD9CM') AND TARGET_DOMAIN_ID = 'Observation'

For records from PATICD_PROC.ICD_CODE and PATICD_DIAG.ICD_CODE:where ICD_VERSION=10 QUERY: SOURCE TO STANDARD SELECT TARGET_CONCEPT_ID FROM CTE_VOCAB_MAP WHERE SOURCE_VOCABULARY_ID IN ('ICD10CM') AND TARGET_DOMAIN_ID = 'Observation'

For PAT.MART_STATUS, OBSERVATION_CONCEPT_ID=4053609

For PAT.PATTYPE, OBSERVATION_CONCEPT_ID=40769091

When operation time observation values then 3016562|| |OBSERVATION_DATE|PATBILL.SERV_DATE
VISIT_OCCURRENCE.VISIT_START_DATE OR VISIT_OCCURRENCE.VISIT_START_DATE|If observation is from PATBILL use service date
If observation comes from PAT.MS_DRG, PATCPT.CPT_CODE, PATICD_PROC.ICD_CODE, PATICD_DIAG.ICD_CODE then use visit start date

For operation time observation, a combination of procedure date and visit start date unless the procedure date is greater than the end of the month|| |OBSERVATION_DATETIME|-|NULL|| |OBSERVATION_TYPE_CONCEPT_ID|-|38000281 Observation recorded from EHR with text result|| |VALUE_AS_NUMBER|||| -|VALUE_AS_STRING|PAT.MART_STATUSPAT.POINT_OF_ORIGIN
PAT.DISC_STATUS
PAT.PAT_TYPE|Value_as_string only populated for Premier-specific fields mart_status, point_of_origin, disc_status, and pat_type
Marital status values populated directly from PAT.MART_STATUS as ‘M’, ‘S’, ‘O’, or ‘U’
select point_of_origin_desc from poorgin pojoin pat p on p.mart_status=po.point_of_origin

select disc_status from poorgin pojoin pat p on p.mart_status=po.point_of_origin

select pat_type_desc from pattype pjoin pat p1 on p1.pat_type=p.pat_type|Use look up values in the text fields.| +|VALUE_AS_STRING|PAT.MART_STATUS
PAT.PAT_TYPE|Value_as_string only populated for Premier-specific fields mart_status and pat_type
Marital status values populated directly from PAT.MART_STATUS as ‘M’, ‘S’, ‘O’, or ‘U’


select pat_type_desc from pattype pjoin pat p1 on p1.pat_type=p.pat_type|Use look up values in the text fields.| |VALUE_AS_CONCEPT_ID|PATCPT.CPT_COD
PATBILL.STD_CHG_CODE
PATICD_PROC.ICD_CODEPAT
ICD_DIAG.ICD_CODE |same rules as for concept_id and source_concept_id, but use 'Maps to value' relationship|| |QUALIFER_CONCEPT_ID|-|NULL|| |UNIT_CONCEPT_ID|-|For operation time records 8550 Else NULL|Set UNIT_CONCEPT_ID = NULL when the source unit value is NULL;Set UNIT_CONCEPT_ID = 0 when source unit value is not NULL but doesn't have a mapping| @@ -48,6 +48,9 @@ The field mapping is performed as follows: |UNITS_SOURCE_VALUE|-|NULL|| |QUALIFIER_SOURCE_VALUE|-|NULL|| +### 27-Sept-2024 +- Removed admitting source and discharge destination from cdm.observation + ### 03-Mar-2024 - Added Surgery (concept_id=3016562) From 36f457d2755e2bb5a07930ec258ec21c76c29ac7 Mon Sep 17 00:00:00 2001 From: sgasmanjj Date: Wed, 16 Oct 2024 13:44:46 -0400 Subject: [PATCH 4/6] Update Premier_Visit_Occurrence.md --- docs/PREMIER/Premier_Visit_Occurrence.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/PREMIER/Premier_Visit_Occurrence.md b/docs/PREMIER/Premier_Visit_Occurrence.md index a6f32957..44d8d78b 100644 --- a/docs/PREMIER/Premier_Visit_Occurrence.md +++ b/docs/PREMIER/Premier_Visit_Occurrence.md @@ -30,7 +30,7 @@ Admitting and discharge information is captured in Premier as the place of servi |VISIT_SOURCE_CONCEPT_ID|-||| |ADMITTING_SOURCE_CONCEPT_ID|PAT.POINT_OF_ORIGIN|if POINT_OF_ORIGIN then ADMITTING_SOURCE_CONCEPT_ID
0 then 8976
1 then 8844
2 then 8716
3 then 8844
4 then 8717
45 then 581384
46 then 8650
5 then 8863
6 then 8844
7 then 8870
8 then 8844
9 then 8844
A then 8761
B then 8536
C then 8536
D then 8717
E then 8883
F then 8546
G then 8844
|| |ADMITTING_SOURCE_VALUE|PAT. POINT_OF_ORIGIN|PAT. POINT_OF_ORIGIN|| -|DISCHARGE_TO_CONCEPT_ID|PAT.DISC_STATUS|If DISC_STATUS then DISCHARGE_TO_CONCEPT_ID
1 then 8536, 2 then 8844
3 then 8863, 4 then 8863
5 then 8844, 6 then 8536
7 then 8844, 8 then 8536
9 then 8717, 20 then NULL
21 then 8844, 30 then 8844
40 then 8546, 41 then 8546
42 then 8546, 43 then 8966
50 then 8546, 51 then 8546
61 then 8863, 62 then 8920
63 then 8970, 64 then 8676
65 then 8971, 66 then 581379
69 then 8844, 70 then 8844
71 then 8844, 72 then 8717
81 then 8536, 82 then 581379
83 then 8863, 84 then 8827
85 then 8844, 86 then 8536
87 then 8844, 88 then 8966
89 then 8863, 90 then 581379
91 then 581379, 92 then 8676
93 then 8971, 94 then 581379
95 then 8844, 99 then 8844
|| +|DISCHARGE_TO_CONCEPT_ID|PAT.DISC_STATUS|If DISC_STATUS then DISCHARGE_TO_CONCEPT_ID
1 then 8536, 2 then 8844
3 then 8863, 4 then 8863
5 then 8844, 6 then 8536
7 then 8844, 8 then 8536
9 then 8717, 20 then NULL
21 then 8844, 30 then 8844
40 then 0, 41 then 0
42 then 0, 43 then 8544
50 then 8546, 51 then 8546
61 then 8863, 62 then 8920
63 then 8970, 64 then 8676
65 then 8971, 66 then 581379
69 then 8844, 70 then 8844
71 then 8844, 72 then 8717
81 then 8536, 82 then 581379
83 then 8863, 84 then 8827
85 then 8844, 86 then 8536
87 then 8844, 88 then 8844
89 then 8863, 90 then 581379
91 then 581379, 92 then 8676
93 then 8971, 94 then 581379
95 then 8844, 99 then 0
|| |DISCHARGE_TO_SOURCE_VALUE|PAT.DISC_STATUS|PAT.DISC_STATUS|| |PRECEDING_VISIT_OCCURRENCE_ID|VISIT_OCCURRENCE.VISIT_OCCURRENCE_ID|For a given person, find the visit prior to this one and reference it here|A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit| From 030109ef3c11619021f3e7b88309c630741f8c77 Mon Sep 17 00:00:00 2001 From: sgasmanjj Date: Wed, 16 Oct 2024 13:51:29 -0400 Subject: [PATCH 5/6] Update Premier_Visit_Occurrence.md --- docs/PREMIER/Premier_Visit_Occurrence.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/PREMIER/Premier_Visit_Occurrence.md b/docs/PREMIER/Premier_Visit_Occurrence.md index 44d8d78b..2ee32f2c 100644 --- a/docs/PREMIER/Premier_Visit_Occurrence.md +++ b/docs/PREMIER/Premier_Visit_Occurrence.md @@ -28,13 +28,14 @@ Admitting and discharge information is captured in Premier as the place of servi |CARE_SITE_ID|PAT.PROV_ID||| |VISIT_SOURCE_VALUE|PAT.I_O_IND||| |VISIT_SOURCE_CONCEPT_ID|-||| -|ADMITTING_SOURCE_CONCEPT_ID|PAT.POINT_OF_ORIGIN|if POINT_OF_ORIGIN then ADMITTING_SOURCE_CONCEPT_ID
0 then 8976
1 then 8844
2 then 8716
3 then 8844
4 then 8717
45 then 581384
46 then 8650
5 then 8863
6 then 8844
7 then 8870
8 then 8844
9 then 8844
A then 8761
B then 8536
C then 8536
D then 8717
E then 8883
F then 8546
G then 8844
|| +|ADMITTING_SOURCE_CONCEPT_ID|PAT.POINT_OF_ORIGIN|if POINT_OF_ORIGIN then ADMITTING_SOURCE_CONCEPT_ID
0 then 8976
1 then 8844
2 then 8716
3 then 8844
4 then 8717
45 then 581384
46 then 8844
5 then 8863
6 then 8844
7 then 8870
8 then 8844
9 then 0
A then 8761
B then 8536
C then 8536
D then 8717
E then 8883
F then 8546
G then 8844
|| |ADMITTING_SOURCE_VALUE|PAT. POINT_OF_ORIGIN|PAT. POINT_OF_ORIGIN|| |DISCHARGE_TO_CONCEPT_ID|PAT.DISC_STATUS|If DISC_STATUS then DISCHARGE_TO_CONCEPT_ID
1 then 8536, 2 then 8844
3 then 8863, 4 then 8863
5 then 8844, 6 then 8536
7 then 8844, 8 then 8536
9 then 8717, 20 then NULL
21 then 8844, 30 then 8844
40 then 0, 41 then 0
42 then 0, 43 then 8544
50 then 8546, 51 then 8546
61 then 8863, 62 then 8920
63 then 8970, 64 then 8676
65 then 8971, 66 then 581379
69 then 8844, 70 then 8844
71 then 8844, 72 then 8717
81 then 8536, 82 then 581379
83 then 8863, 84 then 8827
85 then 8844, 86 then 8536
87 then 8844, 88 then 8844
89 then 8863, 90 then 581379
91 then 581379, 92 then 8676
93 then 8971, 94 then 581379
95 then 8844, 99 then 0
|| |DISCHARGE_TO_SOURCE_VALUE|PAT.DISC_STATUS|PAT.DISC_STATUS|| |PRECEDING_VISIT_OCCURRENCE_ID|VISIT_OCCURRENCE.VISIT_OCCURRENCE_ID|For a given person, find the visit prior to this one and reference it here|A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit| ## Change Log: +* 2024.10.16: Updated mappings for discharge_to and admitted_from concept_ids to better represent source data. * 2024.03.12: Updated VISIT_CONCEPT_ID * 2023.10.23: Updated visit logic, the exact date of visits is now available. * 2021.08.11: Updated VISIT_TYPE_CONCEPT_ID to leverage standard concept id. From 8095a51aeee797b4ae976c541eeba16621214d41 Mon Sep 17 00:00:00 2001 From: sgasmanjj Date: Thu, 17 Oct 2024 08:01:37 -0400 Subject: [PATCH 6/6] Update Premier_Visit_Occurrence.md --- docs/PREMIER/Premier_Visit_Occurrence.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/PREMIER/Premier_Visit_Occurrence.md b/docs/PREMIER/Premier_Visit_Occurrence.md index 2ee32f2c..ecb833d5 100644 --- a/docs/PREMIER/Premier_Visit_Occurrence.md +++ b/docs/PREMIER/Premier_Visit_Occurrence.md @@ -30,7 +30,7 @@ Admitting and discharge information is captured in Premier as the place of servi |VISIT_SOURCE_CONCEPT_ID|-||| |ADMITTING_SOURCE_CONCEPT_ID|PAT.POINT_OF_ORIGIN|if POINT_OF_ORIGIN then ADMITTING_SOURCE_CONCEPT_ID
0 then 8976
1 then 8844
2 then 8716
3 then 8844
4 then 8717
45 then 581384
46 then 8844
5 then 8863
6 then 8844
7 then 8870
8 then 8844
9 then 0
A then 8761
B then 8536
C then 8536
D then 8717
E then 8883
F then 8546
G then 8844
|| |ADMITTING_SOURCE_VALUE|PAT. POINT_OF_ORIGIN|PAT. POINT_OF_ORIGIN|| -|DISCHARGE_TO_CONCEPT_ID|PAT.DISC_STATUS|If DISC_STATUS then DISCHARGE_TO_CONCEPT_ID
1 then 8536, 2 then 8844
3 then 8863, 4 then 8863
5 then 8844, 6 then 8536
7 then 8844, 8 then 8536
9 then 8717, 20 then NULL
21 then 8844, 30 then 8844
40 then 0, 41 then 0
42 then 0, 43 then 8544
50 then 8546, 51 then 8546
61 then 8863, 62 then 8920
63 then 8970, 64 then 8676
65 then 8971, 66 then 581379
69 then 8844, 70 then 8844
71 then 8844, 72 then 8717
81 then 8536, 82 then 581379
83 then 8863, 84 then 8827
85 then 8844, 86 then 8536
87 then 8844, 88 then 8844
89 then 8863, 90 then 581379
91 then 581379, 92 then 8676
93 then 8971, 94 then 581379
95 then 8844, 99 then 0
|| +|DISCHARGE_TO_CONCEPT_ID|PAT.DISC_STATUS|If DISC_STATUS then DISCHARGE_TO_CONCEPT_ID
1 then 8536, 2 then 8844
3 then 8863, 4 then 8863
5 then 8844, 6 then 8536
7 then 8844, 8 then 8536
9 then 8717, 20 then NULL
21 then 8844, 30 then 8844
40 then 0, 41 then 0
42 then 0, 43 then 8844
50 then 8546, 51 then 8546
61 then 8863, 62 then 8920
63 then 8970, 64 then 8676
65 then 8971, 66 then 581379
69 then 8844, 70 then 8844
71 then 8844, 72 then 8717
81 then 8536, 82 then 581379
83 then 8863, 84 then 8827
85 then 8844, 86 then 8536
87 then 8844, 88 then 8844
89 then 8863, 90 then 581379
91 then 581379, 92 then 8676
93 then 8971, 94 then 581379
95 then 8844, 99 then 0
|| |DISCHARGE_TO_SOURCE_VALUE|PAT.DISC_STATUS|PAT.DISC_STATUS|| |PRECEDING_VISIT_OCCURRENCE_ID|VISIT_OCCURRENCE.VISIT_OCCURRENCE_ID|For a given person, find the visit prior to this one and reference it here|A foreign key to the VISIT_OCCURRENCE table of the visit immediately preceding this visit|