1.47.10122020 to 1.59.10282020 - National-Clinical-Cohort-Collaborative/Data-Ingestion-and-Harmonization GitHub Wiki

OMOP Standardized Vocabulary

  • OMOP Standardized Vocabulary tables has been update to version - V5.0 02-OCT-20

OMOP Vocabularies included in this update:

  • ICD10CM - International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)

  • NUCC - National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC)

  • Revenue Code - UB04/CMS1450 Revenue Codes (CMS)

  • LOINC - Logical Observation Identifiers Names and Codes (Regenstrief Institute)

  • SNOMED - Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)

  • Gender - OMOP Gender

  • NDC - National Drug Code (FDA and manufacturers)

  • RxNorm Extension - RxNorm Extension (OHDSI)

  • SPL - Structured Product Labeling (FDA)

  • RxNorm - RxNorm (NLM)

  • ICD9Proc - International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)

  • ATC - WHO Anatomic Therapeutic Chemical Classification

  • Ethnicity - OMOP Ethnicity

  • CPT4 - Current Procedural Terminology version 4 (AMA)

  • HCPCS - Healthcare Common Procedure Coding System (CMS)

  • CMS Place of Service - Place of Service Codes for Professional Claims (CMS)

  • Currency - International Currency Symbol (ISO 4217)

  • Medicare Specialty - Medicare provider/supplier specialty codes (CMS)

  • Race - Race and Ethnicity Code Set (USBC)

  • ICD9CM - International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)

  • ABMS - Provider Specialty (American Board of Medical Specialties)

  • OMOP Extension - OMOP Extension (OHDSI)

  • CVX - CDC Vaccine Administered CVX (NCIRD)

  • PPI - AllOfUs_PPI (Columbia)

  • The CPT-4 vocabulary is reconstituted to the concept table manually by updating the CPT4 concepts from the UMLS site.

PCORnet CDM

Patient Encounter with Discharge status EX

  • Patient with discharge status of EX are insert into Observation Domain with the following concepts: OBSERVATION _CONCEPT_ID = 4216643 'Patient died' OBSERVATION_TYPE_CONCEPT_ID = 44818516 (EHR discharge status 'Expired')/ Note this is Death Type but it is non-standard in Athena.

ValueSet updates

  • The p2o_term_xwalk table is merged and contains all of the valueSet mapping data elements for PCORnet CDM, including the result_qual values and blood type vaues.
  • If the result_qual is NI, UN or OT then the value_as_concept_id is set to NULL, not mappable, meaning it is interpreted as there is no value.

Blood Types

  • In some site, the blood type result are submitted in the raw_result column with OT in the result_qual. For those cases, the values in the raw_result are mapped against the newly added blood type concept_ids for LOINC ='882-1'.
lab result text string to match target concept id
A 4008253
A NEG 46237061
A Negative 46237061
A POS 46238174
A Positive 46238174
A+ 46238174
A- 46237061
AB 4013993
AB NEG 46237994
AB Negative 46237994
AB POS 46237873
AB Positive 46237873
B 4009006
B NEG 46237872
B Negative 46237872
B POS 46237993
B Positive 46237993
O 4237761
O- 46237435
O+ 46237992
O NEG 46237435
O Negative 46237435
O POS 46237992
O Positive 46237992
AB- 46237994
AB+ 46237873