concepts and conditions

Overview

Questions

• What is an OMOP concept ?
• Where are patient conditions stored in OMOP ?

Objectives

• Understand that nearly everything in a hospital can be represented by an OMOP concept_id.
• Know that OMOP data usually includes the OMOP concept table and other data from the vocabularies
• Be able to look up concepts by their name
• Know that patient conditions are stored in the condition_occurrence table

Introduction

---

Nearly everything in a hospital can be represented by an OMOP concept_id.

Any column within the OMOP CDM named *concept_id contains OMOP concept IDs. An OMOP concept_id is a unique integer identifier. Concept_ids are defined in the OMOP concept table where a corresponding name and other attributes are stored. OMOP contains concept_ids for other medical vocabularies such as SNOMED and LOINC, which OMOP terms as source vocabularies.

concept table columns	Description
concept_id	Unique identifier for the concept.
concept_name	Name or description of the concept.
domain_id	The domain to which the concept belongs (e.g. Condition, Drug).
vocabulary_id	The vocabulary from which the concept originates (e.g. SNOMED, RxNorm).
concept_class_id	Classification within the vocabulary (e.g. Clinical Finding, Ingredient).
standard_concept	‘S’ for standard concepts that can be included in network studies
concept_code	Code used by the source vocabulary to identify the concept.
valid_start_date	Date the concept became valid in OMOP.
valid_end_date	Date the concept ceased to be valid.
invalid_reason	Reason for invalidation, if applicable

Looking up OMOP concepts

---

OMOP concepts can be looked up in Athena an online tool provided by OHDSI.

TODO provide a challenge to look up a concept in Athena TODO add a challenge to look up the same concept in one of the synthea datasets TODO add briefly about concept relationships

TODO ? add about the condition_occurrence table to make the episode longer and give something for concept to refer to

Key Points

• Understand that nearly everything in a hospital can be represented by an OMOP concept_id.
• Know that OMOP data usually includes the OMOP concept table and other data from the vocabularies
• Be able to look up concepts by their name
• Know that patient conditions are stored in the condition_occurrence table