Simon Jupp

Technical coordinator, Ontology project lead, European Bioinformatics Institute (EMBL-EBI)

Simon oversees the development of the EMBL-EBI’s “Semantics as a Service” platform that aims to make it easier for scientists, database curators and application developers to work with ontologies and semantically enrich biological metadata. He has a special interest in the advancement and use of semantic technologies to improve how we publish and share data on the web, and how to develop smarter applications to harness this enriched data.

He is the technical lead for the GWAS catalog that houses data on associations between small variations in the human genome and complex disease and he is actively involved in the development of metadata models and standards for projects including the Human Cell Atlas project and the European Joint Programme on Rare Diseases.

Simon’s team develop the Experimental Factor Ontology (EFO) which is an application ontology designed to pull a number of different ontology standards together and tailor them for the needs of an individual application or database. EFO ensures public data held at EMBL-EBI is interoperable and aligned with community standards, and it provides the core ontology for linking diseases to potential drug targets in the OpenTargets platform.

Simon’s team also develop services for hosting hundreds of public ontologies and tools for mapping between ontologies and annotating metadata with ontologies. These services are essential to support the large-scale curation of often messy data and have enabled millions of data points to be connected for further downstream analysis by the scientific community.

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My Sessions

Ontology Services for the Biomedical Sciences

Educational Room

Ontologies and Semantic Web technologies play an important role in the life sciences to help make data more interoperable and reusable. There are now many publicly available ontologies that enable biologists to  describe everything from gene function through to animal physiology and disease. Various efforts such as the Open Biomedical Ontologies (OBO) foundry provide central […]

Life Sciences Track