Samples, Phenotypes and Ontologies

The Samples, Phenotypes and Ontologies team, led by Helen Parkinson, is organised into three themes: High throughput mammalian phenotyping, Semantics as a Service and two human genetics resources, the GWAS Catalog and the PGS Catalog (in Collaboration with Cambridge colleagues Mike Inouye and Sam Lambert). The team is part of the Molecular Archives Cluster and works closely with cluster colleagues on the Human Cell Atlas, CINECA, Covid19 Portal.

Model Resources and Mouse Informatics

Led by Coordinator Jeremy Mason (IMPC), and Project Lead Zina Perova (PDX and Organoids) we develop international infrastructure for mammalian model phenotypic and omics data archiving, integration and dissemination. The team is a partner on several international projects, including: The International Mouse Phenotyping Consortium (IMPC), KOMP2, INFRAFRONTIER-I3PDXIntegrator and IPAD-MD. All these externally funded projects share a common theme of data integration of rich phenotypic data derived from model species to better understand gene function and how genetic variation contributes to disease. 

Semantic Data Integration

Henriette Harmse leads the teams semantic data integration team delivering ontologies and tools such as OLS as well as the development components of the GWAS Catalog. The team's semantic interoperability tools are used by EBI Data Archives and Knowledge Bases, including the GWAS Catalog, OpenTargets, pharma and agrifood companies and are ELIXIR Recommended Interoperability Resources

GWAS Catalog

Led by Project Leads Laura HarrisJackie MacArthur and Yomi Mosaku the team delivers the infrastructure and content for the GWAS Catalog, an NHGRI funded resource, summarising 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.

Collaborations

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, the National Institutes of Health and OpenTargets. These range from data analysis and generation projects such as IMPC and projects which are mainly infrastructural such as CORBEL, EOSCLife and EJP CoFund and EXCELERATE. We work closely with ELIXIR as members of the ELIXIR Interoperability Platform and developers of ELIXIR deposition databases. 

In collaboration with partners in the KOMP2 project and the International Mouse Phenotyping Consortium, the team manages, analyses, and distributes complex phenotypic data from 20,000 knockout mouse lines and, promotes mouse data integration internationally via the IMPC. The team also develops open-source software tools for managing data, developing and integrating ontologies and data, and works with semantic web technologies.

The team actively develops ontologies including the Cell Type Ontology and Experimental Factor Ontology and delivers Ontology Lookup Service, an ontology search and cross referencing tool.

We collaborate closely with Melissa Haendel and Chris Mungall of Monarch, an integration project for genotype/phenotype data, by supplying human and mouse phenotypic data and using their tools in delivery of the IMPC portal. We consume the Uberon Ontology - a critical integrative resource for vertebrate anatomy used across EBI's sample representation and the MONDO Disease Ontology.

Annual reports

  • Parkinson team, 2012
  • Parkinson team, 2011
  • Parkinson team, 2010