odysseusinc / circe-be

CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5

Circe-be

Introduction

A Java library used to create queries for the OMOP Common Data Model v5.0-v5.3. These queries are used in cohort definitions (CohortExpression) as well as custom features (CriteriaFeature).

Features

• Defines an object model for domain-specific queries (eg: Condition occurrence), correlated criteria (at least N records between X days before and Y days after) and concept set expressions
• Defines an object model for cohort definitions (CohortExpression) where the cohort is defined by Cohort Entry Events, Inclusion Rules and Cohort Exit Strategy. Resulting episodes are combined into non-overlapping periods of time.
• Generate Negative Control cohorts from a Concept Set expression
• Import a cohort expression from a JSON file and rehydrates the CohortExpression object.
• A suite of unit tests using an embedded instance of Postgres 9.6 to validate proper specification.

Getting Started

Add dependency (and repository) to maven:

  <repositories>    
    <repository>
      <id>ohdsi</id>
      <name>repo.ohdsi.org</name>
      <url>http://repo.ohdsi.org:8085/nexus/content/repositories/releases</url>
    </repository>
  </repositories>
  <dependencies>
    <dependency>
      <groupId>org.ohdsi</groupId>
      <artifactId>circe</artifactId>
      <version>1.9.0</version>
    </dependency>
  </dependencies>    

License

Circe is licensed under Apache License 2.0