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Database Management CLI

The OMOP CDM instantiation tool provides a streamlined way to bootstrap a local OHDSI Common Data Model (CDM) database using Athena vocabulary files and synthetic test data.

Verbosity flag placement

The --verbose / -v flag is a global option and must appear before the subcommand name, not after it:

omop-graph -v relationship-classification ...   # ✓ correct
omop-graph relationship-classification -v ...   # ✗ flag is ignored

Use -v for INFO level and -vv for DEBUG level.

omop-cdm

Moved to omop-maint

Vocabulary loading was previously exposed as omop-graph omop-cdm. It is now provided by the OMOP_Alchemy package under the omop-maint CLI.

Load Athena vocabulary CSV files from a configured source path into the OMOP CDM database using the ORM staged CSV loader.

populate_with_test_data

This command adds synthetic patient data into the OMOP CDM after populating the vocabularies using omop-maint load-vocab-source

relationship-classification

This command ingests pre-defined relationship classifications and mappings into the database. It categorizes standard OMOP relationships into semantic groups (e.g., Hierarchical, Lateral, Mapping) to enable more intelligent graph reasoning.

Rationale

The standard OMOP relationship table provides basic metadata, but lacks unified semantic "kinds" out of the box. This tool maps those relationships to a specific PredicateKind (like HIERARCHY, IDENTITY, or ASSOCIATION) and provides detailed inference descriptions used by the KnowledgeGraph facade.

Prerequisites

  1. Prepopulated OMOP CDM (e.g. using omop-maint load-vocab-source)
  2. omop-graph configured via oa-configurator (omop-config configure omop_graph, see Getting Started: Configuration); the CDM connection is resolved from OmopGraphConfig.cdm_db, no environment variables involved.

  3. A directory containing:

    • predicate_classification.csv: Defines the semantic classes and subclasses (descriptions, semantics, and inference rules).
    • predicate_mapping.csv: Maps specific OMOP relationship_ids to the classes defined in the classification file.

    Pass this directory via --pred-class-dir below.

Usage

omop-graph relationship-classification --pred-class-dir <PATH_TO_CSV_DIR>

Command Options

Option Short Type Default Description
--pred-class-dir String Required Path to the directory containing the classification CSVs.
--verbose -v Count 0 Increase logging verbosity (use -v or -vv).