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AMIA 2020 Workshop Summary.pdf
Advanced i2b2 Topics Shawn Murphy MD, Ph.D. Mass General Brigham and Harvard Medical School November 14th, 2020 i2b2 Star Schema can adapt to Multiple Fact Tables FACT TABLES Patient (dimension) Visit (dimension) Adapts to OMOP Connect to OMOP by building ontology of OMOP standard concepts Use Ontology TablesRe: 342. Import CSV
The ObjectID is the same as the PatientID, but the file is imported using modifiers instead. This way more than one row per patient is allowed. Wait, what? Observations that are not modifiers can have more than one row per patient. In fact, a patient usually has multiple diagnoses, meds, orders, etc. recorded duringJune Meeting ETL.pdf
databases for IRB reasons, even though this requires much more storage. Single v. multiple fact tables (new i2b2 option) ◦ BIDMC uses a single fact table … fact tables. This ingestion process has two main issues to over come, first is the use of || as the separator, coming from supplied .dat files SecondOMOP
The legacy i2b2 data model is comprised of a central fact table (observation_fact) surrounded by multiple dimension tables (star schema). In the Observation Medical Outcomes Partnership (OMOP) Clinical Data Model (CDM) rather than a central fact table, we have a collection of them distinguished by domain: proceduresData Storage
The i2b2 data is stored in a relational database, usually either Oracle or SQL Server and always in a star schema format. A star schema contains one fact and many dimension tables. The fact table contains the quantitative or factual data, while the dimension tables contain descriptors that further characterizeRe: AUG Email 2011-Oct
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rows in the Ontology table, which have data encoded for them in the fact table, are actually present in the CONCEPT_DIMENSION table. If there is a row … a LOOKUP table which does not qualify as a DIMENSION because it doesn’t strictly support the fact table. However, there are several codes in the observation facti2b2OMOP_installGuide.pdf
-on-FHIR tools that rely on the i2b2 API are also able to run on the OMOP data model. The standard i2b2 data model is comprised of a central fact table … ), rather than a central fact table, we have a collection of them distinguished by domain: procedures, condition, drug, measurement, observation, etc. In this project