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MSDW Release Notes

Discover what is new in the Mount Sinai Data Warehouse (MSDW). Questions, comments, or bug reports can be submitted through our ticketing portal.

 

Current Version

MSDW Version 2.0.221209 – December 9, 2022

Fixed
  • Most of the blood pressure vital signs in the OMOP measurement table were linked to the wrong encounter records in the OMOP visit_occurrence table.
  • The column invalid_reason in the OMOP concept, concept_relationship, and drug_strength tables sometimes contained an empty string instead of the NULL value, as specified by OHDSI.  The data-load process was updated to restrict allowed values to ‘D’, ‘U’, and NULL only.
  • The column standard_concept in the OMOP concept table sometimes contained an empty string instead of the NULL value, as specified by OHDSI.  The data-load process was updated to restrict allowed values to ‘S’, ‘C’, and NULL only.

 

MSDW Version 2.0 – December 7, 2022

What’s New
  • At our customers’ request, all encounter records from Epic are now included in the OMOP visit_occurrence table, even the “chart documentation events” that aren’t face-to-face or telehealth patient encounters.  Because this approach deviates from OHDSI’s guidance for the visit_occurrence table, these documentation “encounter” records have visit_concept_id = 0.
Changed
  • The 18 foreign key columns in the OMOP visit_occurrence table that matched the naming pattern etl_*_version_id have been removed.  Similarly, the 12 data lineage columns from Epic Caboodle matching the pattern etl_epic_*_key have been removed (but not the ones like etl_epic_*_durable_key).
Future Removals
  • The foreign key columns in all OMOP tables that match the following naming pattern etl_*_version_id are deprecated and will be removed in an upcoming release.
    • If you are using these columns, please update your SQL queries to use the durable *_id columns in conjunction with the etl_record_version_start_datetime and etl_record_version_end_datetime columns.
  • OMOP death table
    • Death date is in the OMOP person table, and OHDSI wants to put cause of death, if available, in the OMOP condition_occurrence table
  • Columns to be renamed in the OMOP visit_occurrence and visit_detail tables:
    • Admitting_source_concept_id renamed as Admitted_from_concept_id
    • Admitting_source_value renamed as Admitted_from_source_value
    • Discharge_to_concept_id renamed as Discharged_to_concept_id
    • Discharge_to_source_value renamed as Discharged_to_source_valu
Unresolved
  • In the OMOP visit_occurrence table, the column xtn_visit_type_source_concept_id is not yet populated to denote “Chart Documentation Event” records
  • Some historical patient addresses are not getting marked as “inactive” when they are replaced by a new address record
  • Epic’s documentation records that appear in the diagnosis and procedure master files aren’t yet re-assigned to OMOP’s observation table (from condition_occurrence and procedure_occurrence, respectively)

 

Release Notes Archive

Release History

The overview of Mount Sinai Data Warehouse OMOP Release Notes. For a detailed explanation of release history, refer to the Archive.

 

MSDW2 Version Release Date Summary
2.0.221209 Dec 9, 2022 Fixed columns and encounter records
2.0 Dec 7, 2022 Added all Epic encounter records
1.10.221204 Dec 4, 2022 Updated drug_exposure table
1.10.221123 Nov 23, 2022 Updated ATHENA vocabularies to Oct 31, 2022 version
1.10.221109 Nov 9, 2022 Bug fix in MEASUREMENT, data pipeline enhancement
1.10.221104 Nov 4, 2022 Data pipeline enhancement
1.10.221030 Oct 30, 2022 Bug fix in DRUG_EXPOSURE
1.10.221028 Oct 28, 2022 Data pipeline enhancement
1.10.221020 Oct 20, 2022 Data pipeline enhancement
1.10 Oct 19, 2022 Added flowsheet records to OBSERVATION
1.9.221015 Oct 15, 2022 Bug fix in multiple OMOP tables
1.9 Oct 7, 2022 Added flowsheet records to MEASUREMENT
1.8.220930 Sep 30, 2022 Updated ATHENA vocabularies to Aug 29, 2022 version
1.8.220929 Sep 29, 2022 Data pipeline enhancement
1.8.220916 Sep 16, 2022 Data pipeline enhancement
1.8.220915 Sep 15, 2022 Bug fix in OBSERVATION and NOTE
1.8.220909 Sep 9, 2022 Bug fix in FACT_RELATIONSHIP
1.8 Aug 26, 2022 Added BioMe BioBank cohorts to OBSERVATION, Epic value sets to CONCEPT_RELATIONSHIP
1.7 Aug 19, 2022 Added cancer patient cohort to OBSERATION, new views PATIENT_ALLERGY_XTN and COHORT_MEMBERSHIP_XTN
1.6.220811 Aug 11, 2022 Data pipeline enhancement
1.6.220727 Jul 27, 2022 Bug fix in NOTE
1.6.220720 Jul 20, 2022 Bug fix in CONCEPT_SYNONYM
1.6.220701 Jul 1, 2022 Bug fix in PROCEDURE_OCCURRENCE
1.6.220624 Jun 24, 2022 Data pipeline enhancement
1.6.220610 Jun 10, 2022 Data pipeline enhancement
1.6.220607 Jun 7, 2022 Bug fix in PROCEDURE_OCCURRENCE
1.6 May 27, 2022 Added flowsheet-inferred procedures to PROCEDURE_OCCURRENCE, up to six provider specialties to PROVIDER_ATTRIBUTE_XTN
1.5.220513 May 13, 2022 Bug fix in MEASUREMENT and FACT_RELATIONSHIP
1.5.220506 May 6, 2022 Added CDC race & ethnicity code mappings to CONCEPT_RELATIONSHIP
1.5.220502 May 2, 2022 Bug fix in OBSERVATION
1.5.220415 Apr 15, 2022 Added Cancer Institute Biorepository cohort to OBSERVATION
1.5.220408 Apr 8, 2022 Added Imaging Research Warehouse cohort to OBSERVATION
1.5 Mar 25, 2022 Added BioMe BioBank cohort to OBSERVATION
1.4.220314 Mar 14, 2022 Bug fix in VISIT_OCCURRENCE
1.4 Feb 22, 2022 Added standarized race, ethnicity, and combined race & ethnicity to OBSERVATION
1.3 Jan 27, 2022 Added patient allergies to OBSERVATION
1.2 Nov 30, 2021 Added immunizations to DRUG_EXPOSURE, patient demographics to OBSERVATION
1.1 Sep 30, 2021 Added clinical notes to NOTE, family history to OBSERVATION
1.0 Sep 20, 2021 Launch of MSDW2 OMOP!
 
 
 

Supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.