Document Control Authors and Contributors Name Organization Title Patrick Ryan OMOP Co-Investigator Don Griffin CSC Senior Data Architect Christian Reich OMOP Program Manager, IT Implementation Shesh Mudiyanur CSC Data Architect Cortney Hayflinger OMOP Programmer Aurelia Ford CSC Informaticist Mark Khayter Ephir Documentation Specialist Reviewers Name Role Title Date Reviewed Peter Parsons Technical Writer Principal 02-Aug-2009 Aurelia Ford CSC Informaticist 02-Aug-2009 Vicki Fan CSC Business Analyst 25-Aug-2009 Document References Document Title Type of Reference Document Location OMOP CDM ETL Mapping Specification Business Rules OMOP Basecamp OMOP CDM ETL Technical Specification Detail Technical Information OMOP Basecamp Change Record Date Author Version Change Reference 02-Aug-2009 Shesh Mudiyanur 1.0 New document, describes OMOP Common Data Model Specification. 23-Sep-2009 Sanjay Dharmadhikari Mark Khayter 2.0 Modified to reflect renamed Column names Added License page Modified data examples Background The Observational Medical Outcomes Partnership (OMOP) is a public-private partnership designed to protect human health by improving the monitoring of drugs for safety and effectiveness. The partnership, which began in the fourth quarter of 2008, is conducting a two-year research initiative to determine the
Condition Occurrence types are determined for Condition Eras, based on a 30-day persistence window, as follows: Condition Occurrence Type Condition Occurrence Type Description 65 Condition Era, 30 day persistence window The sample CONDITION_ERA table is constructed from the condition data based on a 30-day persistence window, indicated by a CONDITION_OCCURRENCE_TYPE of “Era, 30-Day Persistence.” The sample representation of the above data in the CONDITION_ERA table follows. Condition Era ID Condition Start Date Person ID Confidence Condition End Date Condition Concept ID Condition Occurrence Type Condition Occurrence Count 4197598 121107 4197598 63 1 31967 29-JUL-2003 127260 4197598 63 2 CONDITION_OCCURRENCE_REF The Condition Occurrence Reference reflects the indicator(s) from which the Condition Occurrence was drawn or inferred, and indicates whether a condition (diagnosis) was primary or secondary and the relative positioning within a Person’s condition record. A detailed listing of the Condition Occurrence Types is included in . Field Data Type Required Description and Notes VARCHAR(3) YES The code indicating the type of Condition Occurrence. Condition Occurrence Type is used to define the source data indicators from which the Condition was identified, the level of standardization, and the type of occurrence. Conditions Types are defined as Primary/Secondary Diagnosis, Problem Report, and Person Status (including Mortality when available in the source data). A detailed listing of Condition Occurrence Types is recorded in VARCHAR(120) YES A detailed description of the Condition Occurrence Type. Valid values include Diagnosis from Inpatient Claims, Diagnosis from Outpatient visits, Diagnosis from ER visits, etc.
Field Data Type Required Description and Notes INTEGER YES A unique identifier for the Clinical Description. CONCEPT_ID INTEGER YES A foreign key to a Concept stored in the Concept table of the Dictionary. DESCRIPTION_NAME VARCHAR(1000) YES The text of the term used to describe the Concept associated with the Description. Example of Loaded Table The following example illustrates the representation of Descriptions associated with a SNOMED-CT Concept “Chronic Atrial Fibrillation’. The Concept can be described in the following ways: Concept Code: 426749004 Concept Fully Specified Name: Chronic atrial fibrillation (disorder) Preferred Term for the Concept: Chronic atrial fibrillation Source Vocabulary: SNOMED_CT Description Status: Current for both Preferred Term and Fully Specified Name If the Fully Specified Name for the Concept is used as the Concept Name in the Concept entity, then the preferred term is stored as a Synonym in the Synonym entity. The particulars for the Synonym being added are as follows: Concept ID: 3409069 Concept Synonym ID: 3351850 Description Name: Chronic atrial fibrillation Concept Synonym ID Concept ID Description Name 3409069 4141360 Chronic atrial fibrillation CONCEPT_REIONSHIP The Concept Relationship entity stores the relationship between two Concepts. The relationships described in the CDM are directional and are intended to include a Source Concept and a Target Concept with an explicit relationship from Source to Target. Concept Relationship includes many different types of relationships between Concepts. The type of relationships described between Concepts includes the following: Hierarchical or ”ISA” Relationships (Subsumes relationships), which are used to define a direct hierarchies between Concepts. Only the hierarchy relationships between two closest Concepts are captured in the Relationship table. All the Ancestor and descendent relationships that are not immediate parent-child relationships are recorded in the Concept Ancestor table. The hierarchical relationships can be between Concepts that are adopted from the same Vocabulary source or between Concepts adopted from difference Vocabulary sources. The Relationship Type attribute is used to identify various types of relationships that are captured in the Concept Relationships table.