Mapping of EFO terms from the GWAS catalog data to multiple ontologies at the Rat Genome Database.

Abstract

The laboratory rat, Rattus norvegicus, is an important model of many human diseases, and experimental findings in the rat have relevance to both human physiology and disease. The Rat Genome Database (RGD, https://rgd.mcw.edu/) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, cellular components, and chemical interactions for genes, quantitative trait loci (QTL), and strains. Because the laboratory rat is used often as a model of human physiology and disease, RGD has incorporated data from the NHGRI-EBI (National Human Genome Research Institute-European Bioinformatics Institute) catalog of human genome-wide association studies (GWAS) (https://www.ebi.ac.uk/gwas/). This provides the basis for easy integration of RGD data for rat and other species with human SNP (single nucleotide polymorphism)-phenotype associations. When data from different sources use different vocabularies, there must be some standard way to compare the data. Since the human GWAS data are annotated with Experimental Factor Ontology (EFO) terms, RGD needed to map those EFO terms to various ontologies used at RGD for annotating rat genomic and strain data, so the human data can be translationally associated with the wealth of preclinical data including rat genes, rat QTL, and rat strains. To bridge the ontology/vocabulary gap, the curators at RGD have mapped all the EFO terms (http://www.ebi.ac.uk/efo) used to annotate the human GWAS SNPs in the NHGRI-EBI Catalog of human GWAS Catalog Data (https://www.ebi.ac.uk/gwas/) to multiple ontologies used at RGD. RGD has used the mappings to translate human GWAS disease/phenotype EFO annotations into RGD Disease Ontology annotations, human phenotype ontology annotations, clinical measurement ontology annotations, and vertebrate trait ontology annotations. Also, RGD has made the ontological mappings available via Simple Standard for Sharing Ontological Mappings (SSSOM) files on the RGD download site (https://download.rgd.mcw.edu/ontology/mappings/).