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MSDW Release Notes History

Review the archive of updates in the Mount Sinai Data Warehouse (MSDW). Questions, comments, or bug reports can be submitted through our ticketing portal.

 

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)

 

Version 1.10.221204 – December 4, 2022

Fixed
  • Some patient records that were previously merged in Epic were not logically deleted from the OMOP person table
Changed
  • Updated data-integration ETL framework for loading the OMOP drug_exposure table from Caboodle’s several medication-related tables.  To be safe, all medication records in Epic were reloaded to the OMOP drug_exposure table.

 

Version 1.10.221123 – November 23, 2022

What’s New

 

Version 1.10.221109 – November 9, 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.
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

 

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

 

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

 

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

 

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

 

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)

 

Version 1.9.221015 – October 15, 2022

Fixed
  • In some cases, the records in OMOP tables pertaining to patients switching from regulatory non-protected status to protected status were not getting updated to match.  The OMOP person table did not exhibit this problem.

 

Version 1.9 – October 7, 2022

What’s New
  • New data: A new set of numerical measurements from flowsheets, including pulmonary function test (PFT) results (OMOP measurement table)
Fixed
  • Vital signs recorded with decimals — like height, weight, and body temperature — were being improperly rounded to the nearest integer (OMOP measurement) (as reported in patch 1.8.220909)
  • The user-access views for OMOP data marts configured with an “exclusion override” still had some records incorrectly auto-excluded in certain cases.
  • The OMOP drug_exposure table was reloaded from Caboodle to ensure that no historical records are missing
Changed
  • Enhancements to process for loading and updating value sets (OMOP concept_relationship table)
  • 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)

 

Version 1.8.220930 – September 30, 2022

What’s New
Changed
  • Enhanced data pipeline for the ATHENA vocabulary files and all manually created data files
  • Enhanced, parameter-driven framework for loading data files
  • Full change history is now being captured for the OMOP visit_occurrence table
  • Updates to etl_record_source table
Unresolved
  • Vital signs recorded with decimals — like height, weight, and body temperature — are being improperly rounded to the nearest integer (OMOP measurement)
  • 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

 

Version 1.8.220929 – September 29, 2022

Changed
  • Full change history is now being captured for the OMOP measurement table
Unresolved
  • Vital signs recorded with decimals — like height, weight, and body temperature — are being improperly rounded to the nearest integer (OMOP measurement)
  • 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

 

Version 1.8.220916 – September 16, 2022

Changed
  • Full change history is now being captured for the OMOP observation and note tables
Unresolved
  • Vital signs recorded with decimals — like height, weight, and body temperature — are being improperly rounded to the nearest integer (OMOP measurement)
  • 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

 

Version 1.8.220915 – September 15, 2022

Fixed
  • Some records in OMOP tables observation & note were not being logically deleted when their corresponding patient records in the OMOP person table were logically deleted (due to patient record merges in Epic)
Unresolved
  • Vital signs recorded with decimals — like height, weight, and body temperature — are being improperly rounded to the nearest integer (OMOP measurement)
  • 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

 

Version 1.8.220909 – September 9, 2022

Fixed
  • The records in OMOP fact_relationship linking the systolic and diastolic blood pressure measurements in the OMOP measurement table were being duplicated (OMOP fact_relationship table)
Changed
  • Full change history is now being captured for the OMOP procedure_occurrence and condition_occurrence tables
Unresolved
  • Vital signs recorded with decimals — like height, weight, and body temperature — are being improperly rounded to the nearest integer (OMOP measurement)
  • 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

 

Version 1.8 – August 26, 2022

What’s New
  • New data:
    • The value sets defined in Epic (also called “VCG groupers”) for the following seven master files: diagnoses (EDG), procedures (EAP), surgical procedures (ORP), lab components (LRR), medications (ERX), flowsheet rows (FLO), and immunizations (LIM) (OMOP concept_relationship table)
    • Indicator for patient membership in the following three additional BioMe Biobank cohorts (OMOP observation table):
      • BioMe Biobank Global Diversity Array (Sema4)
      • BioMe Biobank Global Screening Array (Regeneron)
      • BioMe Biobank Whole Exome Sequencing (Regeneron)
Fixed
  • Some telehealth visits were previously incorrectly classified as outpatient visits (OMOP visit_occurrence table)
  • The chart documentation events for telephone notes were previously incorrectly classified as telehealth visits (OMOP visit_occurrence table)
  • The OMOP condition_occurrence table was reloaded from Caboodle to ensure that no historical records are missing
Changed
  • Deployment of a new record versioning framework, for capturing full change history, with the OMOP procedure_occurrence table as the first implementation (other OMOP tables will follow in subsequent releases)
  • Record versioning was enabled on the audit log table for the user-access views (UAVs)
  • Additional flowsheet rows (pulmonary function tests, PHQ-9 depression screening) were added to the Epic VCG grouper 122788 which filters MSDW’s data extraction from Caboodle’s flowsheet fact table; these data will be integrated into the OMOP measurement and observation tables in an upcoming release
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)

 

Version 1.7 – August 19, 2022

What’s New
  • New extension views patient_allergy_xtn and cohort_membership_xtn to more easily query these types of records from the OMOP observation table
  • New data:
    • A new pre-calculated cohort called “Cancer Patient Cohort” comprising all Mount Sinai patients with a diagnosis in Epic that maps to a cancer-related ICD-9, ICD-10, or SNOMED code (OMOP observation table and cohort_membership_xtn view)
Fixed
  • Reloaded the missing records from the OMOP concept_synonym table (as reported in patch 1.6.220811)
  • Removed duplicated mappings from Epic’s race & ethnicity categories to their corresponding standard CDC race & ethnicity codes (OMOP concept_relationship table)
Changed
  • Enhancements to process for loading and updating inferred procedures (see release notes for version 1.6)
  • Enhancements to process for loading and updating the links between systolic and diastolic blood pressure measurements (OMOP fact_relationship table)
  • Enhancements to the audit process for tracking changes to all user-access views
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 telehealth visits are being incorrectly classified as outpatient visits (OMOP visit_occurrence table)
  • The telehealth category of encounter records incorrectly includes telephone notes (OMOP visit_occurrence table)
  • 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)

 

Version 1.6.220811 – August 11, 2022

Changed
  • Enhancement to the data-load process to handle more than one unique identifier for certain records, such as locations in Epic’s EAF master file
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
  • Some records are missing from OMOP’s concept_synonym table as a result of patch 1.6.220720

 

Version 1.6.220727 – July 27, 2022

Fixed
  • After updating the data extraction code, all of Caboodle’s clinical notes were reloaded to OMOP’s note table
Unresolved
  • Some historical patient addresses are not getting marked as “inactive” when they are replaced by a new address record

 

Version 1.6.220720 – July 20, 2022

Fixed
  • Removed corrupted Unicode characters in OMOP’s concept_synonym table
Unresolved
  • Some historical patient addresses are not getting marked as “inactive” when they are replaced by a new address record

 

Version 1.6.220701 – July 1, 2022

Fixed
  • Procedure events loaded from E/M codes and level of service codes now correctly classified as “General Procedure” in OMOP’s procedure_occurrence table (they were previously uncategorized)
 

 

Version 1.6.220624 – June 24, 2022

Changed
  • Deployment of an automated process to retrieve the DICOM header data elements for imaging studies from the Imaging Research Warehouse (IRW)
  • Enhancements to the code for loading procedures (Epic’s EAP master file) and surgical procedures (Epic’s ORP master file) to OMOP’s concept table

 

Version 1.6.220610 – June 10, 2022

Changed
  • Enhancements to the process for loading vocabulary files from OHDSI’s ATHENA repository (https://athena.ohdsi.org) and other data files
  • Enhancements to the process for loading and updating concept mappings (OMOP concept_relationship table)
  • Deployment of a “rules engine” framework for automating data-quality checks in MSDW

 

Version 1.6.220607 – June 7, 2022

Fixed
  • Updated code to ensure that any changes to inferred procedures (ECMO, renal dialysis) are properly captured (OMOP procedure_occurrence table)

 

Version 1.6 – May 27, 2022

What’s New
  • New data:
    • Up to six specialties for each Mount Sinai provider, as loaded to Epic (OMOP provider_attribute_xtn table)
    • Extracorporeal membrane oxygenation (ECMO) and renal dialysis procedures inferred from flowsheet documentation (OMOP procedure_occurrence 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
  • 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).

 

 

 

Version 1.5.220513 – May 13, 2022

Fixed
  • Updated code to ensure that all blood pressure measurements always include both the systolic and diastolic portions (OMOP measurement and fact_relationship tables)

 

Version 1.5.220506 – May 6, 2022

What’s New
  • New data:
    • Epic’s ethnic group, ethnic background, and race category values mapped to standard CDC race and ethnicity codes (OMOP concept_relationship table with relationship_id = ‘Maps to non-standard’)

 

Version 1.5.220502 – May 2, 2022

Fixed
  • Removed patient demographics records consisting of empty strings or no responses (OMOP observation table)

 

Version 1.5.220515 – April 15, 2022

What’s New
  • New data:
    • Indicator for patient membership in the Cancer Institute Biorepository (CIB) data set (OMOP observation table)

 

Version 1.5.220408 – April 8, 2022

What’s New
  • New data:
    • Indicator for patient membership in the Imaging Research Warehouse 1.0 (IRW) data set (OMOP observation table)

 

Version 1.5 – March 25, 2022

What’s New
  • New data:
    • Indicator for patient membership in BioMe Biobank data set (OMOP observation table)
Changed
  • New framework for loading patient membership in non-Epic research data-set cohorts
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
  • 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).

 

 

Version 1.4.220314 – March 14, 2022

Fixed
  • ED visits (without hospitalization) previously misclassified as hospital outpatient visits

 

Version 1.4 – February 22, 2022

What’s New
  • New data:
    • Patient races standardized to CDC race codes (OMOP observation table)
    • Patient ethnicities standardized to CDC ethnicity codes (OMOP observation table)
    • Mount Sinai Combined Race & Ethnicity variable (OMOP person and observation tables)
    • Additional social history variables: years of tobacco use, illicit drug frequency, alcohol oz per week (OMOP observation 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
  • 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).

 

 

Version 1.3 – January 27, 2022

What’s New
  • New data:
    • Patient allergies (OMOP observation table)
Future Removals
  • The following columns have been deprecated and will be removed in a future release:
    • The foreign key columns in all OMOP tables that match the following naming pattern: etl_*_version_id
  • 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
  • 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).

 

 

Version 1.2 – November 30, 2021

What’s New
  • New data:
    • Immunizations (OMOP drug_exposure table)
    • Patient demographics: race, ethnicity, marital status, sexual orientation, gender identity, preferred language, religion (OMOP observation table)
Future Removals
  • 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
  • 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).

 

 

Version 1.1 – September 30, 2021

What’s New
  • New data:
    • Clinical notes (OMOP note table)
    • Lab component result notes (OMOP note table)
    • Family history (OMOP observation table)
Future Removals
  • 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
  • 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).

 

Version 1.0 – September 20, 2021

What’s New
  • Launch of MSDW2 OMOP with the following data from Epic Caboodle:
    • Patient demographics (OMOP person and death tables)
    • Providers (OMOP provider table)
    • Mount Sinai organization hierarchy, including facilities, clinics, locations, departments, other care sites (OMOP care_site and location tables)
    • Encounters of all types (OMOP visit_occurrence table)
    • Diagnoses from encounters and problem list (OMOP condition_occurrence table)
    • Lab test component results (OMOP measurement table)
    • Vital signs (OMOP measurement table)
    • Medication administrations and dispenses (OMOP drug_exposure table)
    • Procedures (OMOP procedure_occurrence table)
    • Past medical history (OMOP observation table)
    • Surgical history (OMOP observation table)
    • Social history (OMOP observation table)
    • Epic master files: diagnosis, medication, procedure, lab component, flowsheet row, category lists (OMOP concept table)
Future Removals
  • 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
  • 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).
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