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 1.10.221123 – November 23, 2022

What’s New

 

MSDW Version 1.10.221109 – November 9, 2022

Changed
  • Updated data-integration ETL framework (for loading OMOP tables) to handle large volumes of Caboodle table backfills from Mount Sinai’s Epic upgrade on Sunday, November 6, 2022
Fixed
  • Some vital sign measurements from April 2022 were missing due to a bulk update in Caboodle at the end of March 2022 (as reported in patch 1.6.220811).  To be safe, all vital signs in Epic were reloaded to the OMOP measurement table.

 

MSDW Version 1.10.221104 – November 4, 2022

Changed
  • Updated data-extraction ETL framework to handle large volumes of Caboodle table backfills from Mount Sinai’s Epic upgrade on Sunday, November 6, 2022

 

MSDW Version 1.10.221030 – October 30, 2022

Fixed
  • Duplicate records in the OMOP care_site and location tables due to a bug in the load process for the state abbreviations lookup table (as reported in patch 1.10.221028
  • The decimal places of the numeric values in the following columns in the OMOP drug_exposure table were being rounded to the nearest integer:
    • quantity
    • xtn_verbatim_quantity
    • xtn_order_dose_range_low
    • xtn_order_dose_range_high
    • xtn_calculated_dose_range_low
    • xtn_calculated_dose_range_high
  • Duplicate records in the OMOP care_site and location tables due to a bug in the load process for the state abbreviations lookup table (as reported in patch 1.10.221028

 

MSDW Version 1.10.221028 – October 28, 2022

Changed
  • Full change history is now being captured for the OMOP provider and provider_attribute_xtn tables
Unresolved
  • A bug in the load process for the state abbreviations lookup table created duplicate records in the OMOP care_site and location tables when it was reloaded on Oct 20, 2022

 

MSDW Version 1.10.221020 – October 20, 2022

Changed
  • Further enhancements to the parameter-driven framework for loading data files
  • Incorporated the loading of patient observations and assessments from flowsheets (OMOP observation table) into the nightly scheduled ETL framework

 

MSDW Version 1.10 – October 19, 2022

What’s New
  • New data: A new set of patient observations and assessments from flowsheets, including the PHQ-2 and PHQ-9 depression screening results (OMOP observation table)
Changed
  • Additional enhancements to process for loading and updating concept mappings from Usagi and manually created spreadsheets (OMOP concept_relationship table)
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_value
Unresolved
  • Some historical patient addresses are not getting marked as “inactive” when they are replaced by a new address record
  • Due to a bulk update that occurred in Caboodle at the end of March 2022, some vital signs records are missing from April 2022 in OMOP’s measurement table
  • 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 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
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!
 
 
 

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