2 Sentinel Quality Assurance Package

This documentation describes Sentinel Quality Assurance Program Package 8.6.0. This program package is used by the Sentinel Operations Center (SOC) for data quality assurance (QA) review and characterization of the Sentinel Distributed Database (SDD). To create the SDD, each Data Partner (DP) transforms local source data into Sentinel Common Data Model (SCDM) format. The SOC uses a set of data quality review and characterization programs to ensure that the SDD meets reasonable standards for data transformation consistency and quality. This version of the QA program package queries SCDM version 8.0.0 and 8.1.0 tables.

Table 2.1 describes the modification history of this package.

Table 2.1: QA Package History of Modifications
Version Date Modification
8.6.0 02/23/2023

Refactored the Level 1 Module to improve package runtime by reducing the number of times the QA Package Level 1 Module reads Data Partner SCDM tables.

Introduced new FlagType NOTE:

  • In intances where an SCDM variable is optional and not populated, CheckID 111 will now write flag NOTE intead of WARN
  • msoc/all_l1_l2_flags sort order logic is modified to push NOTE flags to bottom of dataset

Mother-Infant Identification Updates:

  • Removed requirement for Data Partner to have at least one year of data available before package begins identifying infants
  • Relaxed infant enrollment criteria to at least 1 day in the first three years of life
  • Relaxed mother enrollment requirements from 180 days of prior enrollment to 90

Minor Package Modifications and Bug Fixes

8.5.2 12/15/2022

Resolves an issue which caused the package to exclude Mothers and Infants whose RACE = “M” from the results.

8.5.1 12/01/2022

CheckID 223 and 228 Modifications

This release adds or modifies the following flags:

  • PRE_2_07_00-0_223: In the Prescribing table, when Rx_CodeType = ND, Rx must be all digits.
  • DIS_2_03_00-0_223: In the Dispensing table, when Rx_CodeType = ND, Rx must be all digits.
  • DIS_2_03_00-0_228: In the Dispensing table, when Rx_CodeType = ND an Rx code length of ≥ 9 and ≤ 11 is now enforced.

Minor Package Modifications and Bug Fixes

  • Updated the MIR module to prevent the package from aborting when BIRTHTYPE = 6.
8.5.0 09/22/2022

CheckID 223 and 228 Modifications

This release adds or modifies the following flags:

  • PRE_2_07_00-0_228: In the Prescribing table, when Rx_CodeType = GP an Rx code length of 14 is now enforced. This flag is a warn.
  • DIA_2_06_00-0_223: In the Diagnosis table, when Dx_CodeType = 09 or Dx_CodeType = 10, a warn flag is thrown if Dx contains a decimal. This flag is a warn.
  • PRO_2_06_00-0_223: In the Procedure table, when Px_CodeType = 09 or Px_CodeType = 10, a warn flag is thrown if Px contains a decimal. This flag is a warn.

DIA_2_06_00-0_228 and PRO_2_06_00-0_228 have been modified to enforce the following new valid lengths:

  • Px_CodeType = 09, Px length ≥ 3 and ≤ 4
  • Dx_CodeType = 09, Dx length ≥ 3 and ≤ 5
  • Dx_CodeType = 10, Dx length ≥ 3 and ≤ 7

CheckID 111 Modifications

Previously, the QA Package would issue a FAIL if the Data Partner did not have at least one observation for in any of the following variables:

  • RxSup and RxAmt in the Dispensing Table
  • Result_Loc in the Lab Results Table
  • EncType and Orig_TransProd in the Inpatient Transfusion Table

As these variables are considered optional by the Sentinel Common Data Model (SCDM), these flags have been downgraded to WARN.

CheckID 121 Modifications

The following values are considered valid by the SCDM, but were missing from the QA Package:

  • In the Lab Results Table, Px_CodeType now accepts the following valid values:

    • CP = Canadian Classification of Diagnostic, Therapeutic, and Surgical Procedures (CCP)
    • CX = Canadian Classification of Health Interventions (CCI)
    • OT = Other

  • In the Prescribing table, Rx_CodeType now accepts the following valid value:

    • AT= Anatomical Therapeutic Chemical Classification (DK)

The following values do not appear in the SCDM and have been removed as valid values from the QA Package:

  • In the Diagnosis table, Dx_CodeType no longer accepts the value C0
  • In the Lab Results Table, Px_CodeType no longer accepts the value CV

Lab Results Table LOINC Value Updates

In response to the August 2.73 LOINC release, the QA Package has been modified

Additional Bug Fixes

This release fixes an issue where the table names for the PRM and PRS tables were not being written to qa_cc_metadata. This would cause Common Components to fail at Data Partners populating those tables.

8.4.1 06/08/2022 New features / enhancements:
  • Minor Input file updates to allow numeric lab values associated with COVID Antibody MS_Test_Names
  • The package will no longer fail and abort on LAB_1_22_00-0_111 (MS_Result_N has no values) when run by Data Partners populating only COVID Labs with character based results
8.4.0 06/02/2022 New features / enhancements:
  • SCDM 8.1.0 Compliance Updates:
    • The QA Package now allows the value M for multi-racial in the Demographic Table’s Race variable
    • Adds new valid MS_Test_Names: SARS_COV_2_AB_TOTAL, SARS_COV_2_AB_A, SARS_COV_2_AB_G, SARS_COV_2_AB_M, SARS_COV_2_AB_AM, SARS_COV_2_AB_GM, SARS_COV_2_AB_NS, UNMAPPED
    • Introduces a new lookup file lkp_lab_loincs.sas7bdat, mapping SOC Approved LOINCS to their corresponding MS_Test_Name
    • Introduces a new set of CheckID 222 Flags: LAB_2_07_[TestID]_222 which warn if MS_Test_Name does not correspond with the appropriate SOC Approved LOINC value
    • Introduces a new set of CheckID 222 Flags: LAB_2_[VarID]_99-U_222 which fail and cause the QA Package to abort in instances where MS_Test_Name is set to UNMAPPED and the following variables do not contain the appropriate value corresponding with Unknown: Modifier, Specimen Source, Fast Ind, Stat, Pt_Loc, Abn_Ind, and Result_Type
    • Flag LAB_2_07_99-U_220 will cause the QA Package to abort if MS_Test_Name is set to UNMAPPED but LOINC is not populated
    • Introduces a new set of CheckID 111 Flags: PRE_1_[VarID]_00-0_111 which cause cause the QA Package to abort if the following variables are not populated in the Prescribing Table: RxSup, RxAmt, RxDoseQuantity, RxFreqQuantity
    • The QA Package will return three new Level 3 tables for characterizing Unmapped LOINCS:
      • lab_l3_unmap_loinc_all: This dataset contains 1-way frequencies for all LOINCS where MS_Test_Name is UNMAPPED
      • lab_l3_n_unmap_loinc_agegrp_sex: This dataset contains frequencies of the top 5000 LOINCS where MS_Test_Name is UNMAPPED, stratified by agegroup and sex
      • lab_l3_n_unmap_loinc_ym: This dataset contains frequencies of the top 5000 LOINCS where MS_Test_Name is UNMAPPED, stratified by year-month
    • SCDM 8.1.0 introduces new key variable combinations for several tables. The new unique row definitions enforced by the package are:
      • Encounter: EncounterID
      • Diagnosis: EncounterID, DX_CodeType, DX, ProviderID
      • Procedure: EncounterID, PX_CodeType, PX, ProviderID
      • Lab Result: LabID
      • Inpatient Pharmacy: RxID
      • Inpatient Transfusion: TransID
      • Prescribing: PrescribingID
8.3.5 03/10/2022 New features/enhancement:
  • Modifies Check 223 to allow alphabetic character M or U as the fifth character in a PRO code when Px_CodeType is C4
  • Addition of valid value SK for px_codetype in LAB and PRO tables.
8.3.4 01/27/2022 New features/enhancement:
  • Modifies Check 223 to allow alphabetic character A as the fifth character in a PRO code when Px_CodeType is C4.
8.3.0 12/16/2021 New features/enhancement:
  • Adds a new dataset dis_l2_rx_rxtype_spec with combinations of Rx, RxType, and Provider Specialty.
  • • Modifies Check 223 to prevent erroneous warns for PRO Table Code Types C2 and C3 based on presence of alphabetic characters F and T, respectively, as the fifth character in a code
  • Adds logic which will abort the package if the ETL number specified in the SCDM Tables Labels does not align with the expected ETL number
8.2.0 11/18/2021 New features/enhancement:
  • Implement ability to QA Rapid COVID Freshest Feasible SDD
  • New QA Package Dataset enc_l2_byvar_dates returns distribution of ENC adate stratified by EncType.
  • CheckID 116 updated from warn to an abort.
  • Minor Package updates
8.1.1 11/10/2021 Minor Package Updates
8.1.0 10/21/2021 New features/enhancement:
  • Addition of .U as an valid value for unknown / missing values in certain Prescribing Table variables
  • New QA Package Dataset vit_l3_pt_ym_stat returning statistics from VIT tables
  • New QA Package Dataset re_l2_rx_rxtype_spec stratifying PRE records by rx, rx_codetype, and Provider Specialty
  • New CheckID 116 which checks FORMATL from PROC CONTENTS results to ensure the formatted value of any ID will not cause downstream issues
8.0.0 09/23/2021 New features/enhancement:
  • Add L2 checks for valid variable combinations of EncType, DDate, Discharge_Disposition, Discharge_Status in Encounter table
  • Add L2 checks to validate new PX_CodeType CV
7.3.0 08/14/2021 New features/enhancement:
  • New table outputting age in days as of earliest enrollment start for infants.
  • Minor package improvements and updates
7.2.1 A minor update to the lab look-up files fixing issue where new COVID Lab LOINCs provided to Data Partners had been omitted.
7.2.0 07/29/2021 New features/enhancement:
  • Addition of CheckIDs 236 and 237: These checks ensure that DTH records have one and only one underlying cause of death.
  • Minor package Updates and improvements
7.1.0 07/01/2021 New features/enhancement:
  • Addition of dia_l2_dx_dxtype_spec, which replaces dia_l2_dx_dxtype. This dataset adds provider specialty (spec) to strata.
  • Addition of pro_l2_px_pxtype_spec which replaces pro_l2_px_pxtype. This dataset adds provider specialty (spec) to strata.
  • Addition of Check 208, which will replace 114 and confirms length of numeric variable is not longer than is needed after confirming this length is the same across SCDM tables
7.0.3 02/27/2021 • Minor package changes for input files only for inpatient tables to enable use of internal dataset
7.0.2 01/29/2021 • Minor maintenance version to address Prescribing table Check ID 120; no longer aborts package.
7.0.1 01/22/2021 • Minor maintenance version to address Prescribing table Check ID 111; no longer aborts package.
7.0.0 04/01/2020 • L1/L2/L3 flags for SCDM v8.0.0 model compliance in existing tables
• Update select L1/L2/L3 flags for SCDM v8.0.0 model compliance in existing tables
• Add compliance checks and new modules for addition of Prescribing, Provider, and Facility tables to the model.
• Temporary removal of the SCDM Snapshot program functionality until the stand-alone version is updated to be SCDM v8.0.0 compliant.
6.2.0 02/14/2020 • Update SCDM Snapshot functionality
* Include SCDMVer variable/ value in qa_cc_metadata output file for future use in qa_common_components
• Replicate all L2/L3 datasets that contain variable DIS.NDC, breaking creating variable
• Rx_Codetype, populated as ND, and renaming NDC to Rx.
• Incorporate new SAS Option (Option=FMTERR) into the master program file.
6.1.0 12/05/2019 • Add SCDM Snapshot program functionality
• Minor bug fix for LAB CheckID 200
• Change input file control_flow from a SAS dataset (.sas7bdat) to a .csv file for internal request building automation
6.0.0 09/16/2019 • Add inpatient transfusion and inpatient dispensing model compliance checks and distribution statistics
5.0.1 05/15/2019 • Minor bug fix for hardcoded dates in the MI ID program
5.0.0 01/31/2019 • Updated to no longer use CC
• Added metadata output table for use with post-QA CC
• Integrated optional execution of MI ID package
4.2.1 08/28/2018 • Addition of warning flag 121 for negative values in vital signs variables HT, WT, Systolic, and Diastolic
4.2.0 08/10/2018 • Add vital signs module and model compliance checks
4.1.5 07/03/2018 • Minor bug fix in dia_l2_dx_dxtype (introduced in 4.1.4)
4.1.4 05/24/2018 • Bugfix for CheckID 223
• Added missing CheckID 223 for PRO in lkp_all_flags
• Updated temporary dataset name in DIA for CheckID 223
4.1.3 05/10/2018 • Minor bug fixes:
• Corrected missing LAB CheckIDs (223, 23X, 243) from msoc. all_l1_l2_flags
• Corrected record counts in msoc.pro_l3_enctype_pxtype_ym
• Removed lowercase function of DP- specific path in LogChecker module
4.1.1 03/08/2018 • Added missing valid value for PRO.px_codetype in lookup table lkp_all_l1
4.1.0 02/22/2018 • Minor bug fixes
• Optimization of L1 module
4.0.2 11/14/2017 • Minor bug fix
4.0.1 09/2/2017 • Minor bug fixes
4.0.0 04/27/2017 • Major updates
3.3.4 2/16/2017 • Added/modified diagnosis datasets
3.3.3 8/17/2016 • Added/modified core and lab datasets
3.3.2 9/30/2015 • Corrected error in PatID exclusion in Labs Module
3.3.1 9/17/2015 • Corrected error in DEM module
3.3.0 5/1/2015 • Redesign of labs module, addition of core checks
3.2.4 9/23/2014 • Updated program for new RequestID compatibility, fixed bug
3.2.3 9/2/2014 • Implemented minor bug fixes
3.2.2 8/26/2014 • Implemented minor bug fixes
3.2.1 7/25/2014 • Implemented minor bug fixes

Table 2.2 shows the version of the Sentinel Common Data Model for which a given version of the QA Package is compatible.3

Table 2.2: QA Package-SCDM Version Compatibility Chart
QA Package Version SCDM Version Release Date
8.6.0 8.1.0 Feb 2023
8.5.0 8.1.0 Nov 2022
8.4.2 8.1.0 Jun 2022
8.4.1 8.1.0 Jun 2022
8.4.0 8.1.0 Jun 2022
8.3.5 8.0.0 Mar 2022
8.3.4 8.0.0 Jan 2022
8.3.0 8.0.0 Dec 2021
8.2.0 8.0.0 Nov 2021
8.1.1 8.0.0 Nov 2021
8.1.0 8.0.0 Oct 2021
8.0.0 8.0.0 Sep 2021
7.3.0 8.0.0 Aug 2021
7.2.1 8.0.0 Aug 2021
7.2.0 8.0.0 Jul 2021
7.1.0 8.0.0 Jul 2021
7.0.3 8.0.0 Feb 2021
7.0.2 8.0.0 Jan 2021
7.0.1 8.0.0 Jan 2021
7.0.0 8.0.0 Dec 2020

  1. Please Note: The QA Program Package 8.4.x series and greater is backwards compatible with the SCDM 8.0.0 only for Data Partners building the Rapid COVID Distributed Database.↩︎