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ENTITY_MODEL.md

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Entity Model

Tanagra defines a custom object model on top of the underlying relational data. Tanagra's objects are called entities.

An underlay is a collection of entities and the relationships between them that map to an underlying relational dataset. In the Tanagra UI, you work with one underlay at a time (e.g. building cohorts, feature sets, datasets).

Entity

An entity is an object that is displayed in the UI somehow and makes sense to an end user. i.e. If you define an entity X, end users should be able to understand what a list of X is without knowing anything about the underlying database schema.

e.g. For OMOP, the entities include: person, condition, procedure, condition_occurrence, etc.

An entity mapping tells Tanagra how to get a list of the entity instances. Frequently, an entity mapping will just point to a single table. It can also point to a subset of a table or a raw SQL query or view.

e.g. For OMOP, the person and condition_occurrence entities each map to the table of the same name. The condition entity maps to a subset of the rows of the concept table (WHERE domain_id='Condition'). The procedure entity maps to a different subset of the rows of the concept table (WHERE domain_id='Procedure').

Primary Entity

There is a single primary entity for each underlay. This defines what makes up a cohort.

e.g. For OMOP, the primary entity is person and a cohort is a group of person instances.

Attributes

Each entity has a list of attributes or properties. Attributes are used in the UI somehow: display, ordering, etc.

There are 2 types of attributes. A SIMPLE attribute has a single value and a KEY_AND_DISPLAY attribute has both a value and a display name.

Hierarchies

Each entity can have one or more hierarchies. This is used by the UI to display instances in a tree view instead of a list view. Currently, the hierarchy depth is capped at 64 levels, but that's just an arbitrary limit and we could raise it or allow users to override it in the future.

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Entity Group

An entity group indicates a specific relationship between one or more entities. These relationships are pre-defined and tell Tanagra how to convert entity queries into SQL and how to generate useful index tables.

There are currently 2 types of entity groups defined in Tanagra.

GROUP_ITEMS

A GROUP_ITEMS entity group defines a relationship between 2 entities. There is a one-to-many relationship between the GROUP entity and the ITEMS entity.

The UI will ask for instances of the ITEMS entity for a given GROUP instance.

e.g. For OMOP, the GROUP_ITEMS entity group defines the relationship between the brand and ingredient entities. Each brand instance contains one or more ingredient instances. The UI will ask for instances of ingredient for a given brand (e.g. ingredients in Tylenol PM).

CRITERIA_OCCURRENCE

A CRITERIA_OCCURRENCE entity group defines a relationship between 3 entities. Each OCCURRENCE instance is associated with exactly one CRITERIA instance and one PRIMARY instance. The PRIMARY entity refers to the primary entity of the underlay. There may be multiple OCCURRENCE instances for each CRITERIA and PRIMARY instance.

The UI will ask for:

  • Instances of the OCCURRENCE entity for a given PRIMARY and/or CRITERIA instance.
  • The number of PRIMARY instances that have at least one OCCURRENCE instance for a given CRITERIA instance.

e.g. For OMOP, the CRITERIA_OCCURRENCE entity group defines the relationship between the person, condition, and condition_occurrence entities. The UI will ask for condition_occurrence instances for a given person instance and/or condition instance. The UI will also ask for the number of person instances that have at least one condition_occurrence instance for a given condition instance (e.g. number of people with at least one diagnosis of diabetes).