Delivering databases and interoperability tools for mammalian models of disease, GWAS, PGS and Polygenic Scores.
The Samples, Phenotypes and Ontologies team, led by Helen Parkinson, is organised into two themes, Semantics as a Service and human genetics activities delivering the GWAS Catalog and the PGS Catalog (in Collaboration with Cambridge colleagues Mike Inouye and Sam Lambert). The team is part of the Knowledge Management Section and works closely with colleagues across EMBL-EBI including the Human Cell Atlas, the cohort integration project CINECA, and the Covid19 Portal. We also collaborate in delivery of the eQTL portal and supply content and ontologies to the industry-academia precompetitive OpenTargets project. The team collaborates closely with the Phenomics Team led by Tudor Groza.
David Osumi-Sutherland leads the Ontology Application Team and is leading our work on projects including the Virtual Flybrain, the Human Brain Atlas and HubMap.
Henriette Harmse leads the team’s semantic data integration service delivering FAIR interoperability tools such as the Ontology Lookup Service and the Ontology Cross Reference Service. The team’s FAIR interoperability tools are used by EMBL-EBI Data Archives and Knowledge Bases, including the GWAS Catalog, OpenTargets, pharma and agrifood companies and are ELIXIR Recommended Interoperability Resources.
Laura Harris and Yomi Mosaku lead the content and software activities delivering the infrastructure and content for the GWAS Catalog, an NHGRI funded resource, which summarises data from Genome Wide Association Studies in the form of curated SNP-Trait associations and supporting summary statistics. The GWAS Catalog Team collaborates with OpenTargets to deliver genetic data in support of target prioritisation and provides GWAS data to the European Covid19 portal.
Aoife McMahon, project lead for the Genetic Data Platform, leads our partnership in the EC funded Intervene project which is developing a platform and pipeline for the development and application of PGS at scale across biobanks and integrates the Polygenic Score Catalog.
Members of the team work on ~15 projects with external collaborators where we are funded by the Chan-Zuckerberg Institute (CZI), the European Commission, the BBSRC, the Wellcome Trust, Health Data Research UK, the National Institutes of Health and industry via OpenTargets. Projects range in scope from data analysis and data generation projects and projects delivering infrastructure such as EOSCLife, the European Joint Programme for Rare Diseases and Intervene. We work closely with ELIXIR as members of the ELIXIR Interoperability Platform.
The team actively develops ontologies including the Cell Type Ontology and Experimental Factor Ontology.
