Key Points

What is OMOP?

  • Using a standard makes it much easier to share data
  • OMOP uses concepts to link different tables together
  • The concept table contains humanly readable names for concept_ids

Exploring OMOP concepts with R

  • Concepts have additional attributes such as vocabulary, domain, and standard concept status
  • The concept table can be queried using R to retrieve specific attributes of concepts
  • Concepts can be filtered based on their domain, vocabulary and class
  • Standard concepts are those that are recommended for use in analyses within the OMOP framework

Parquet files

  • Parquet files are a columnar storage file format optimized for big data processing.

  • The arrow package in R can be used to read and manipulate parquet files.

More on concepts

  • OMOP tables contain many concept_ids, usually named with a _concept_id suffix.

  • The concept table can be used to look up humanly readable names for various concept_ids.

  • OMOP tables can be linked using common identifier.

Measurements and Observations

  • Measurements are mainly lab results and other clinical measurement records like pulse rate
  • Observations are other facts obtained through questioning or direct observation
  • Concept ids identify the measure or observation and values are stored in value_as_number or value_as_concept_id
  • We can join to the concept table to find a particular measurement or observation concept by name

Conditions and Visits

  • Conditions are stored in the condition_occurrence table in the OMOP CDM.

  • Visits are stored in the visit_occurrence table and linked to other clinical tables via visit_occurrence_id.

  • A visit represents a period of time during which a patient interacts with the healthcare system and there can be multiple types of visits.

  • Visits may be important to consider in analyses depending on the research question.

Medications

  • Know that exposure of a patient to medications is mainly stored in the drug_exposure table
  • Understand that drug concepts can be at different levels of granularity
  • Understand that source values are mapped to a standard vocabulary
  • Understand how to access the concentration or strength of an exposure using the drug_strength table

Dates and timesDates and times in OMOP

  • Dates and times are used in most tables in the OMOP CDM to record when events happened.

  • They are often used in pairs to record the start and end of an event, which allows us to calculate the duration of that event.