RGD Reference Report - RGD GWAS Catalog Import Pipeline - Rat Genome Database

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RGD GWAS Catalog Import Pipeline

Authors: RGD automated, PIPELINES 
Citation: RGD pipeline to import data from GWAS Catalog and create human variant and QTL records
RGD ID: 151232293
Web Url: https://www.ebi.ac.uk/gwas/docs/file-downloads

Variants reported as significant Genome-Wide Association Study (GWAS) hits were imported from EBI's GWAS Catalog (https://www.ebi.ac.uk/gwas/docs/file-downloads) along with the associated traits, phenotypes and/or diseases. Trait, phenotype and disease associations are initially imported as Experimental Factor Ontology (EFO) terms. RGD curators map those EFO terms to the corresponding terms in ontologies used for other applications in RGD such as the Vertebrate Trait Ontology (VT), Human Phenotype Ontology (HP) and Disease Ontology (DO) to integrate the imported GWAS data with other data in RGD. Based on the GWAS results, corresponding quantitative trait loci (QTL) are also created using the GWAS variant/risk allele as the QTL peak marker. One or more associated "traits" are assigned based on the EFO terms in the GWAS Catalog data. These can be VT, HP or DO terms; in some cases, a clinical measurement (CMO) term might be assigned in addition to or instead of the other possible ontology terms. The associated p-value is stored for each QTL and the position is assigned as the single nucleotide position of the associated variant. QTL symbols are assigned as "GWAS#_H" with "#" being a sequential number based on loading order. The name of the QTL is "[trait name(s)] QTL GWAS#" where "GWAS#" is the same as the QTL symbol. Structured ontology annotations are created for the QTLs based on the EFO IDs from the GWAS_Catalog data and the mapped CMO, VT, HP and/or DO terms (see RGD reference "RGD human GWAS QTL annotation pipeline").