Trait mapping and ontology in the GWAS Catalog
Trait annotation in the GWAS Catalog
Each GWAS included in the Catalog is annotated with a free text field ("Reported trait") summarising the trait under study. The reported trait takes the study design into account and is useful for understanding the specific details of the phenotype, especially in complex studies that include SNP-by-environment interactions, pleiotropy etc, or studies with a background trait (a characteristic that is shared by all participants in a study, but is not directly tested in the association analysis).
Each Reported trait is annotated with one or more ontology terms, reflecting the main trait(s), background trait and any interaction terms.
Ontologies in the GWAS Catalog
All curated trait descriptions (Reported Traits) are mapped to terms from the Experimental Factor Ontology (EFO). Traits in the GWAS Catalog are highly diverse and include diseases, e.g. Type II diabetes, disease markers, e.g. measurements of blood glucose concentration, and non-clinical phenotypes, e.g. hair color. EFO was chosen as the ontology to represent GWAS Catalog traits as it is highly adaptable and extensible, combining parts of several biological domain-specific ontologies and allowing modelling of tests, diseases, anatomy and anthropometry. Accurate mapping of reported traits to EFO terms facilitates searching, visualisation and integration of GWAS Catalog data with other resources.
EFO is freely available in OWL format from the EFO website and can be browsed in the Ontology Lookup Service. Mappings of all GWAS Catalog reported traits to EFO terms are available through our downloads page, along with the GWAS Catalog ontology schema and data knowledgebase.
Interoperability with other ontologies can be achieved using the Ontology Cross Reference Service. Use the service to upload ontology IDs from the GWAS Catalog’s download files.
For an introduction on why we think mapping to ontologies is important, check out this blog post by EFO editor James Malone.
You can find more information on our work so far in our recent Nucleic Acids Research paper.
GWAS Catalog in RDF
Updates of this knowledge base were frozen on 2025-1-30
Each GWAS Catalog data release is also available in OWL/RDF format from our FTP server. The Catalog data can be found in the gwas-kb.owl file while gwas-diagram.owl contains the schema ontology defining the relationships between different Catalog concepts. Please note that the knowledge base file is very large. For this reason, it excludes some Catalog data, such as sample descriptions and ancestry information.
The GWAS Catalog knowledge base is used to generate the GWAS diagram via a Virtuoso triple store. The triple store is currently only available inside EMBL-EBI but will be available publicly in the near future.