Helen Parkinson

Helen Parkinson
Head of Molecular Archival Resources

Dr Helen Parkinson is Head of Molecular Archival Resources at EMBL-EBI comprising several EBI core resources including the European Nucleotide Archive, European Genome-phenome Archive, European Variation BioSamples database. With her faculty colleagues Tony Burdett, Guy Cochrane and Thomas Keane she provides essential databases and infrastructure for open and controlled access data archiving.

Helen leads the Samples, Phenotypes and Ontologies team, delivering databases, data integration tools and ontologies for biomedicine.  Trained as a geneticist, Helen's research focused on Drosophila biology, behaviour, molecular biology and medical genetics. In 1999 she shifted focus to bioinformatics and computational biology while performing positional cloning for primary pulmonary hypertension. Helen's passion is semantic data integration and providing users with useful data. Her team participates extensively in external collaborations ranging from data analysis and generation projects to infrastructural integration projects such as the ELIXIR led initiatives BioMedBridges, CORBEL and EXELERATE and EOSCLife. In collaboration with partners in the KOMP2 project and the International Mouse Phenotyping Consortium, Helen's SPOT team manages, analyses, and distributes complex highthroughput phenotypic data from mammals and promotes phenomic data integration internationally.They also develop open-source software tools for managing data, developing and integrating ontologies and data, and integrating semantic web technologies, these are used in projects such as Open Targets and the IMI project EBiSC.

Prior to joining EMBL-EBI in 2000, Helen was a post-doctoral researcher at the University of Leicester, where she worked on the genetic basis of the genetic disease Primary Pulmonary Hypertension, Hyphophatasia and synteny at human chromosomes 7 and 12. Her PhD thesis examined the temperature compensation of circadian rhythms in Drosophila with Professor Bambos Kyriacou. If she ever goes back to the lab it will be to work on an organism where forward and reverse genetics are tractable.

ORCID iD: 0000-0003-3035-4195

Tel:+44 (0)1223 494 672 / Fax:+44 (0)1223 494 468

Parkinson team

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.

Publications

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Team members

  • Ala Abid
  • Olamidipupo Ajigboye
  • Kolawole Babalola
  • Annalisa Buniello
  • Maria Cerezo
  • Alex Follette
  • Alba Gomez Segura
  • Csaba Halmagyi
  • Henriette Harmse
  • Laura Harris
  • Hamed Haseli
  • James Hayhurst
  • Sajo John
  • Huseyin Kir
  • Samuel Lambert
  • Elizabeth Lewis
  • Federico Lopez Gomez
  • Mauricio Martinez
  • Jeremy Mason
  • James McLaughlin
  • Abayomi Mosaku
  • Violeta Munoz Fuentes
  • David Osumi-Sutherland
  • Zoe Pendlington
  • Zinaida Perova
  • Santhi Ramachandran
  • Mike Relac
  • Shirin Saverimuttu
  • Elliot Sollis
  • Shawn Tan
  • Marta Terán
  • Ross Thorne
  • Emily Tinsley
  • Jonathan Warren
  • Robert Wilson