Disease-Gene association pipeline

Description

Data model for ingesting the Disease-Gene Remote Data Subscription (RDS) set from ONTOFORCE.

Remote data set content

ONTOFORCE’s Disease-Gene Remote Data Subscription set contains unique associations between Diseases (or in general traits) and Genes (or in general targets). These associations are extracted from different public databases (including OpenTargets, GWAS Atlas and GWAS Catalog) and have been mapped together to create a single unified association connected to all different studies and underlying evidence.

For details, see ONTOFORCE’s RDS sets and documentation. To access the data, please reach out to us.

Data model

The pipeline base configures the following data into canonical types:

  1. Disease-Gene Association
    This is the main category containing unique associations between a disease and gene. 

  2. OpenTargets Evidence
    Linking to the Disease-Gene Association category covering underlying evidence per association as reported in the OpenTargets data source.

  3. GWAS Catalog Study
    Linking to the Disease-Gene Association category covering the performed GWAS as reported in the GWAS Catalog source. One study may be linked to multiple associations and vice versa.

  4. GWAS Atlas Study
    Linking to the Disease-Gene Association category covering the performed GWAS as reported in the GWAS Atlas source. One study may be linked to multiple associations and vice versa.

  5. Disease and Phenotype
    Linking to the Disease-Gene Association category as the trait in the association. Mapped with the federated category.

  6. Gene, Protein and Variant
    Linking to the Disease-Gene Association category as the target in the association. Mapped with the federated category.

  7. Publication
    Linking to the Disease-Gene Association category as the literature published on the association and its studies. Mapped with the federated category.

  8. Uncategorized
    Items linked to the Disease-Gene Association category that have no noteworthy category.

For more information, see the Data Ingestion Configuration in the Data tab of your DISQOVER instance.

Download and import

Download the pipeline yml file(s) on your local computer. You can import the file(s) into the DISQOVER Data Ingestion Engine (in a new or existing pipeline) by clicking on the opened pipeline menu bar and choosing import. 

Pipeline_DiseaseGene.yml

Disease-Gene base pipeline to import ONTOFORCE’s published Disease-Gene RDS set.