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SCILHS i2b2 to PCORnet Common Data Model (CDM) tables - SQL and SAS Transforms

Changelog

Jeff Klann, PhD

Changelog

10/8/14 - initial release of preparatory files

10/20/14 - initial release of demographic transform

Version 5 for MSSQL (12/16/14)

12/16/14 - release of "version 5" for SQL Server, which transforms all sections of CDM v1.5 except for unit conversions and code translation on visit_dimension columns.

3/19/15 - release of loyalty cohort transform script

Version 5.1 for MSSQL (8/20/15)

8/20/15 ­ release of "version 5.1" for SQL Server which transforms lab results.

Version 5 for Oracle and 6 for MSSQL (10/15/15)

10/10/15 - release of "version 5" for Oracle, adapted by Wake Forest. Limited to CDM v1.5.2.

10/15/15 - release of "version 6" for SQL Server, which transforms:

  • Vitals 2.0.2: Adds smoking and tobacco status
  • Enrollment: Now adds a flag for loyalty cohort patients
  • Labs v2.0.2
  • Medications v2.0.2 into prescribing and dispensing tables
  • Condition: Uses the CONDITION_SOURCE modifier in Diagnoses 2.0.2
  • Various optimizations and bugfixes noted in the code, plus the following changes requested by the coordinating center:
  • Enrollment date ranges are now based on encounters not facts
  • Discharge disposition: forced to NI for AV
  • Discharge status: forced to NI on AV
  • Encounter columns like admit source now translate null to NI
  • dx_source forced to FI for AV
  • vital_source set to HC

Version 6.1 for MSSQL and v6 for Oracle

12/10/15 - release of "version 6.1" for SQL Server and "version 6" for Oracle:

  • MSSQL and Oracle: Bug fixes in prescribing/dispensing - please re-run
  • MSSQL: Speed optimizations in prescribing, dispensing, labs, condition, and diagnosis. Now each transform runs on 2m patients at Partners in <30m.
  • Note that the Oracle version was adapted by colleagues at Wake Forest and has not been tested by SCILHS Central.

Version 0.6.1 for MSSQL and Oracle (12/17/15)

  • MSSQL and Oracle versions are once again equivalent.
  • Versioning schema changed from 6.x to 0.6.x
  • Migrated to GitHub

Version 0.6.2 for Oracle (1/6/15)

  • Minor bugs fixed in translation from MSSQL to Oracle

Version 0.6.3 for MSSQL (1/13/15)

  • Typos found in field names in trial, enrollment, vital, and harvest tables
  • Enrollment: Basis -> Enr_basis
  • Vital: Vitaliid -> Vitalid
  • Harvest: Speciment_date_mgmt -> Specimen_date_mgmt
  • Pcornet_trial: Trial_id -> Trialid
  • Wrong data type found in pmnprescribing (RX_FREQUENCY)
  • tobbaco_type logic in vitals was faulty