Samples, Phenotypes and Ontologies

The Samples, Phenotypes and Ontologies team, led by Helen Parkinson, is organised into two themes: High throughput mammalian phenotyping and interoperability. The team is part of the Molecular Archives Cluster and shares projects such as the GWAS Catalog with the Genes, Genomes and Variation Cluster. We also collaborate closely with EMBl-EBI colleagues.

Mouse Informatics

Led by Coordinator Terry Meehan, Project Leads Nathalie Conte and Jeremy Mason develops international infrastructure for mammalian phenotypic  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

Simon Jupp 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, the GWAS Catalog, OpenTargets, pharma and agrifood companies and are ELIXIR Recommended Interoperability Resources. 

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 in collaboration with GSK, BioGen, Takeda and the Wellcome Trust Sanger Institute. 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 Gene 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 the Monarch Inititiave, 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.

Annual reports

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