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 three themes: 1. Semantics as a Service, 2, Human Genomics activities delivering the GWAS and PGS Catalogs and 2. IMPC mammalian physiological and MorPhiC cellular models. The team is part of the Knowledge Management Section and works closely with colleagues across EMBL-EBI. We also collaborate in delivery of the eQTL portal and supply data content and ontologies to the industry-academia OpenTargets project.
James McLaughlin leads the Ontology Application Team and is leading our work on agentic ontology development for EFO and other ontologies and the Zooma text to ontology mapping tool.
Henriette Harmse leads delivery of the Ontology Lookup Service (OLS) and the Ontology Cross Reference Service (OXO). 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 Ben Wingfield lead the content and software activities delivering the infrastructure and content for the GWAS Catalog 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 with the Broad Institute’s AMP Knowledge Portal.
The PGS Catalog is delivered in collaboration with Prof Mike Inouye and Prof Sam Lambert at the University of Cambridge and provides open database of polygenic scores and the relevant metadata required for accurate application and evaluation. We collaborate on PGS calculation software: pgs_calc
The International Mouse Phenotyping Consortium (IMPC) is an international effort by 21 research institutions to identify the function of every protein-coding gene in the mouse genome by knocking out every gene and performing broad based phenotyping of male and female mice. The IMPC data analyses, data releases, portal, data archive, APIs and MCP servers are delivered by the team in collaboration with The Mary Lyon Centre’s Director Sara Wells and Prof. Damian Smedley from QMUL. Robert Wilson leads the delivery of the IMPC and MorPhIC.
The MorPhiC program is developing a consistent catalog of molecular and cellular phenotypes for null alleles for every human gene by using in-vitro multicellular systems. The data catalog and cellular models are made available for broad use by the biomedical community. Phase 1 is optimising methods to create null alleles and measure their phenotypic effects in 1,000 protein coding genes. The team delivers data ingest, the data portal and data archive in collaboration with Prof. Stefan Schurer from University of Miami, Prof. Ka Yee Yeung from University of Washington Tacoma and Prof. Damian Smedley from QMUL
