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Geneweaver Data Model

GeneWeaver utilizes a relational normalized data model to store both user data, and external sources data. The database is designed to be flexible and extensible, and to allow for the addition of new data types and analysis tools without requiring changes to the data model.

On a high level the data model uses three schemas to organize the types of data that are stored in the database. The schemas are:

  • production: Geneweaver Application Data
  • odestatic: Static Data
  • extsrc: External Sources Data

This page discusses the concepts and structure of the data model in detail, but is not intended to be used as a reference for the database and data model. For example, this page does not use the actual database table and column names, but instead uses full descriptive name of the entities and their relationships.

Tip

For a complete reference of the Geneweaver data model, see the data model reference page.

Production Schema

The production schema is the primary schema used to store user data. The schema's central entity is the geneset 🧬+📂. The schema contains tables & relationships for user data, but external source and static data relationships utilize tables in the odestatic and extsrc schemas.

erDiagram
    GENESET }o--o| PUBLICATION : hasA
    GENESET }o--|| USER : ownedBy
    GENESET }o--o{ PROJECT: containedIn

ODEStatic Schema

The odestatic schema contains tables for static data, such as species, gene databases, and geneset tier. The schema is used to store data that is not expected to change, and is used to provide a reference for the production schema.

The following diagram shows how the geneset 🧬+📂 entity is related to the odestatic schema entities: species and tier. 

erDiagram
    SPECIES }o--|| GENE_DB : usedBy
    SPECIES ||--o{ GENESET : usedBy
    GENESET }o--|| TIER : isOfA

The odestatic schema also contains tables that are used for internal tracking and configuration. Above, the gene_db entity for the platform, tool, and attribution entities. These entities are used internally by the system to track information about enabled analysis tools, microarray expression platforms, and data sources.

erDiagram
    PLATFORM
    TOOL
    ATTRIBUTION

Extsrc Schema

The extsrc schema contains tables for external sources data, this is where the magic 🪄 happens.

Fundamentally, the gene 🧬 to geneset 🧬+📂 association is a many-to-many association. A geneset can contain many genes, and a gene can be associated with many genesets. To represent this relationship, the association is stored in an associative table, which we call geneset_value.

The gene entity is a polymorphic entity that can be associated with multiple external sources, which are represented by the gene_db entity.

The following diagram shows how the geneset 🧬+📂 entity is related to the extsrc schema entities: geneset_value, gene, and gene_db.

erDiagram
  GENESET_VALUE }o--|| GENESET : isOfA
  GENESET_VALUE }o--|| GENE : isOfA
  GENE ||--o{ GENE_DB : isOfA

Microarray Expression Data

Geneweaver also supports microarray expression data. Due to its complexity, this document does not cover the data model that supports this feature.

For more information on microarray expression data, see the Data Model reference page.