Semantic Web Developer

Key information

  • Location: EMBL-EBI Hinxton
  • Staff category: Staff Member - Technology
  • Contract duration: 1 year 10 months (estimated until 03/09/2022)
  • Grading: 5 (monthly salary starting at £2,738.29 after tax)
  • Closing date: 26 October 2020
  • Reference number: EBI01703

Continue reading for more information about this position, or apply now.

About this position

This is an opportunity to work on the cutting edge of data-driven semantics.

New techniques allow profiling of gene expression, morphology, connectivity and function across massive numbers of cells, allowing us to understand the nature of brain cell types in unprecedented detail.  We are working with the Allen Brain Institute in Seattle, which is at the forefront of this work, to develop a system for sharing their data-driven classifications of brain cells in a broadly accessible form.  This system will include links back to the original data and to systems that other scientists can use to classify cell types from their own data.

Our team at the EBI are experts in using semantics to index and integrate a wide variety of biological data-types, working with projects as diverse as the Human Cell Atlas, the International Mouse Phenotyping Consortium and the Virtual Fly Brain. We are also leading providers of semantic services both within the EBI and to researchers around the world.

Your role

You will be responsible for building a knowledge-graph and API for encoding and sharing data-driven cell-type definitions and classifications.  The knowledge graph and API will be built on an existing system that integrates OWL and Neo4j.

You will work collaboratively with other members our consortium in the US and UK, along with experts at the Allen Brain Institute to:

  • Extend and adapt our knowledge graph fo fit the needs of the project
  • Integrate ontologies and data driven classifications into the knowledge graph
  • Ensure that the API and related exchange standards and software integrate effectively and usefully into standard transcriptomic data analysis pipelines.


You have

  • A strong background in Python development
  • Good, modern DevOps skills for working with and co-ordinating containerised pipelines, ideally including experience with Docker & Dockerhub
  • Good knowledge and experience of shell scripting
  • An interest in semantics, knowledge graphs, ontologies and the semantic web
  • Good working knowledge of Neo4J and/or SPARQL

You might also have

  • Experience with developing APIs in Python
  • Java development experience
  • Experience with using Jenkins
  • A good understanding of OWL
  • An interest in neurobiology


Why join us

EMBL-EBI is a worldwide leader in bioinformatics. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by over 27 member states and two associate member states. We encourage personal and professional development and are committed to ensuring our employees feel valued, supported and empowered to reach their potential at work.

Surrounded by picturesque South Cambridgeshire countryside, our Campus provides employees with a relaxed atmosphere where the pursuit of scientific discovery and meaningful work, underpin every role. In addition, our employees have access to a wide range of benefits including:

  • 30 days annual leave per year plus 8 bank holidays
  • Flexible work arrangements
  • Unique pension scheme including 17% employer contribution
  • Annual salary review
  • Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
  • Death benefit, long-term care, accident at work and unemployment insurances
  • Relocation package including installation grant (if required)
  • On-site library and subsidised on-site gym and cafeteria
  • Casual dress code
  • Free shuttle bus to and from Campus
  • Extensive sports and social club activities (run on campus and remotely)
  • Family benefits: Onsite nursery, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
  • Benefits for non UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance

What else you need to know

 To apply please submit a covering letter and CV through our online system. At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ and individuals from all nationalities. Applications are encouraged from all nationalities and this has continued after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.

This position is limited to the project duration estimated until 03/09/2022. This role is based in Hinxton, UK. More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.

Applications will close at 23:00 GMT on the date listed above.

Appointment will be based on merit alone.