Support for auxiliary OMOP tables

[thomgiles]

Currently CaRROT only supports a limited number of the clinical tables in its data model. Ideal it would support more of the auxiliary tables for OMOP conversion of data similar to usagi.

One table of specific interest is the FACT_RELATIONSHIP table.

The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains.

Examples of Fact Relationships include:

• Person relationships (parent-child)
• Care site relationships (hierarchical organizational structure of facilities within a health system)
• Indication relationship (between drug exposures and associated conditions)
• Usage relationships (of devices during the course of an associated procedure)
• Facts derived from one another (measurements derived from an associated specimen).

All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table:

Ie. Person, 1, Person, 2, parent of Person, 2, Person, 1, child of

There are two stages to this.

1. Support for FACT_RELATIONSHIP conversion in CaRROT CDM
2. Support for the generation of FACT_RELATIONSHIP rules in CaRROT ccom.

[spco]

This does need support, (all tables, not just FACT_RELATIONSHIP). PhilQ made the point that this might best be implemented as a standalone script after CaRROT-CDM, with CaRROT-Mapper only used to map the type of relationship. More exploration is required.

[thomgiles]

the FACT_RELATIONSHIP stuff (especially for MIREDA) should be do-able post ETL. Its more about CaRROT be suitable for conversion of larger clinical cohorts (that may contain a lot more information than is required for cohort discovery activities) into OMOP.