Semantic Web Developer

European Molecular Biology Laboratory (EMBL)

Job Description

We are looking for developer with experience of semantic web technologies to join Molecular Archives group at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK. The developer will contribute to two projects: The Virtual Fly Brain project (VFB) and the Monarch Initiative, both of which deliver biological data integration using shared semantic web technologies.

This semantic web developer position involves the following responsibilities:

  • Development and hardening of biological data pipelines implementing semantic technologies. These pipelines integrate a range of ontologies and diverse data-types from a variety of biomedical data resources into the VFB Knowledge Base.
  • Development and deployment of infrastructure for design-pattern driven development of ontologies for use in the Monarch and VFB projects.

The Virtual Fly Brain project ( is a collaborative effort, funded by the Wellcome Trust, to build a resource that helps Drosophila neurobiologists to explore Drosophila neural circuitry and phenotypes to help inform hypotheses about circuit structure and function and to find the transgenic reagents to test these hypotheses. It integrates 3D image data, phenotypes, transcriptomic and connectomic to allow integrated semantic queries and 3D visualization of neural circuitry and transgenic reagent expression patterns.

The Monarch Initiative ( is a collaborative effort, funded by NIH that integrates controlled phenotypic descriptions and genotype data for humans and all major model organisms. Monarch: provides a portal for exploration of phenotype-based similarity, facilitates identification of animal models of human disease through phenotypic similarity and enables quantitative comparison of cross-species phenotypes.

At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 23 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

Qualifications and Experience

You should have a BSc or MSc in computer science and practical experience of software development and experience with semantic technologies (ideally OWL, RDF, SPARQL, RDF rules, triplestores) as well as more conventional database technologies (SQL). Ideally you will also have experience with Python and Java. Experience with Scala would also be useful, as would experience with graph databases, particularly Neo4J/Cypher.

Good software development practices aimed at developing modular, sustainable software are essential. Experience with standard, distributed version control workflows (ideally with GIT) would be an advantage.

Some background and interest in biology would also be an advantage but is not essential for this post.

The post-holder must possess excellent communication and interpersonal skills and should also work well both independently and within a team environment. The ideal candidate will be able to use their own initiative to create and drive projects to a conclusion.

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