Metadata bioinformatician - European Genome-phenome Archive
Location: EMBL-EBI, Hinxton near Cambridge, UK
Staff Category: Staff Member
Contract Duration: until 31st May 2022
Grading: 5 (monthly salary starting at £2,738.29 after tax)
Closing Date: 9 November 2020
Reference Number: EBI01721
The European Bioinformatics Institute (EMBL-EBI) is seeking a Bioinformatician to join the European Genome-phenome Archive (EGA) to support development and maintenance of the EGA metadata standard, data model, and metadata-related tools.

The EGA is a resource for permanent secure archiving and sharing of all types of potentially identifiable genetic and phenotypic data resulting from biomedical research projects. Its aim is to provide access to data, to foster data re-use, to enable reproducibility, and to facilitate biomedical and translational research in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. The EGA securely archives and provides access to genetic data, frequently streaming over 100TB per day of encrypted data streams to authorized researchers around the world. The EGA is also an ELIXIR Core Data Resource, an active contributor to international standards through the Global Alliance for Genomics and Health, and participates in a variety of EC funded consortia (e.g. EJP-RD, Solve-RD, CINECA, and B1MG).  

Your role

As a Bioinformatician, you will participate in the design, development, and implementation of key components of the EGA metadata standard and data model to ensure data submitted to EGA are compatible with the FAIR principles. You will interact with the EGA Helpdesk and Operations teams and representatives of external consortia for both rare and common diseases to define user requirements, improve the standard, and perform automated metadata curation. Through interactions with the EGA Development team, you will help implement tools and features for improving metadata validation and curation. You will play a key role in ensuring that the EGA collects, stores, and distributes high-quality metadata to approved researchers. The EGA team follows agile methodologies to track work using a mix of the RT ticketing system, JIRA, and Confluence in a highly collaborative environment.

The EGA is part of the EGA/EVA team led by Thomas Keane, part of the Molecular Archives Resources at EMBL-EBI. The successful candidate will collaborate with other EMBL-EBI resources including the Human Cell Atlas and BioSamples, as well as international community standard-setting organisations such as the Global Alliance for Genomics and Health. Initial appointment will be until May 2022 with potential for extension based on successful delivery of the service and external funding availability.

Responsibilities include:
  • Develop, maintain, and improve metadata schemas defining the EGA metadata standard and data model
  • Develop, maintain, and improve user-facing metadata tools and documentation
  • Research and understand EGA data submitter and data requestor use cases to ensure the EGA metadata standard is fit for purpose
  • Plan and perform curation over existing EGA metadata to improve FAIRness
  • Support development of internal metadata processes and integration of these processes with existing production EGA services
  • Help develop and manage metadata databases
  • Ensure EGA metadata standards align with emerging community standards from the Global Alliance for Genomics and Health

You have

You should have the following essential skills and experience:
  • Scripting language frequently used in bioinformatics such as Python or Perl
  • Query language and relational databases such as PostgreSQL, MySQL, or Oracle
  • Familiarity with working in unix environments
  • Familiarity with data processing, ETL processes, managing large datasets
  • Excellent interpersonal and communication skills including strong written and verbal communication in English
  • Experience working in a professional or academic context in multi-person team delivering production services
  • A BSc, MSc, or have equivalent experience in biological sciences, computer science, bioinformatics, or a related field

You might also have

  • Experience working with ontologies
  • Experience working with metadata schemas using formats such as XML or JSON
  • Experience working with human genetic and phenotypic or controlled-access data
  • Experience developing and maintaining APIs

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, with two referees, 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 until 31 May 2022. The role is based in Hinxton, UK and you will be required to relocate if not based locally. There will be a relocation package including installation grant (if applicable). More info on how we are recruiting in this period is available on our page: Recruitment and Onboarding during Covid19.

This will be a busy role with frequently changing priorities. You may from time to time have to attend meetings outside normal working hours and undertake international travel. This role is not suitable for part-time working.

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

Appointment will be based on merit alone.