Ontology Application Coordinator
Ontology Application Coordinator
EMBL-EBI - European Bioinformatics Institute
Hinxton, United Kingdom
Organisation data: Sample Phenotypes & Ontologies
Job Number: EBI02010
Contract Type: Staff Member
Job Function: Coordinator (gr. 8)
Contract Duration-Is this renewable to 9 years?: Yes, funding permitting
Advertised Grade-Grading: Grade 8 (monthly salary starting at £4,103.79 after tax) + benefits
Contract Duration-Length of Time (years/months): 3 years
Closing date: 30 June 2022
About the team/job
You will coordinate projects and personnel within Samples Phenotype & Ontologies Team (SPOT) to deliver new ontology content and semantic services used within EMBL-EBI and as part of multiple international, collaborative projects. The team delivers large data resource projects (GWAS Catalog, PGS Catalog) as well as semantic tools and works across a range of biomedical disciplines including GWAS, high throughput phenotyping, single cell projects and neuroscience. Experience in any of these fields is welcome.
Your role
The team is part of multiple international collaborative projects including Cell Annotation Platform, the Brain Data Standards Initiative, Fly Cell Atlas, The Monarch Initiative and Phenomics First, Open Targets. You will meet regularly with representatives of these projects to determine the nature and direction of work to meet project objectives. You will also participate in meetings with stakeholders and users of these resources as part of workshops etc. to feed their requirements into the team's roadmaps.
You will also
- Design the ontology and ontology tools roadmaps in collaboration with the team leader and senior personnel;
- Supervise the ontology editors, semantic pipeline developers and developers of the EBI semantics as a service tools;
- Work with or collaborators to determine their semantic content and tooling needs, for example, by providing infrastructure and pipelines for ontology integration, and semantically enhanced search, query, and visualisation;
- Set milestones, and track progress of team, draft deliverables and formal progress reports related to milestones;
- Collaborate on authoring grants and papers in collaboration with external collaborators;
- You will meet with groups in EMBL-EBI who use the ontologies and semantic tools developed by the team, to determine how best to meet their needs to enable resource and project delivery for big data project.
You have
- A PhD in Biological Sciences or Bioinformatics demonstrating a broad understanding of biomedical sciences;
- Experience:
- of Biocuration using ontologies;
- of Ontology development (in OWL).
- Experience with schema development for biomedical resources;
- Software development/Scripting experience gained in a biomedical environment ideally in Python;
- Grant writing and/or grant reporting for NIH, EC or UK funders;
- Experience working within a production environment gained in academia or industry;
- Experience of working on large international projects in a coordination role;
- A good understanding of OWL & RDF;
- A firm grasp of good code development practice - VC, testing (via CI), modular development, dependency management;
- Practical Agile development practices and practical experience of defining user stories and communicating these to the developer team;
- Project management experience;
- An understanding of quantitative analysis techniques used by collaborators, for example, omics and/or imaging;
- The ability to:
- write clearly, following scientific writing conventions;
- communicate with and understand the needs of biologists & clinicians.
- Good at managing a diverse team to ensure all are supported sufficiently with training and supervision to carry out their assigned roles.
You might also have
- Masters in Informatics or a higher degree in computer science;
- A good understanding of Neo4j/Cypher;
- Empirical mindset; Basic competency in statistical analysis;
- An understanding of Machine Learning application to biomedical data;
- Experience with single cell biology and/or data analysis;
- Experience with leveraging ontologies and ontology annotation for informatics analysis;
- Experience with clinical data and/or patient records;
- Experience in a service environment gained in academia or industry.
Why join us
Do something meaningful
At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.
Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.
Enjoy lots of benefits
- Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme including 17% employer contribution, death benefit, long-term care, accident-at-work and unemployment insurances;
- Flexible working arrangements;
- Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover);
- Generous time off: 30 days annual leave per year, in addition to eight bank holidays;
- Relocation package including installation grant (if required);
- Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely);
- Family benefits: On-site nursery, 10 days of 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.
For more details please see our employee benefits page.
What else you need to know
- Contract duration: This position is a 3 year contract, with a possibility for renewal to a maximum of 9 years (depending on funding);
- International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants;
- Diversity and inclusion: 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;
- Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you;
- How to apply: To apply, please submit a cover letter and a CV through our online system. We aim to provide a response within two weeks after the closing date.
