About the team/job
This is an exciting opportunity to work at the cutting edge of evidence generation in fast moving field of drug target identification and prioritisation. You will be embedded in a dynamic team working with cloud based technologies, integrating evidence from across EMBL-EBI and other databases to identify and prioritise drug targets.
The scientific literature is a rich source of evidence for the role of potential drug targets in disease, as well as other relationships between targets, disease, drugs, methods and so on. We are developing a robust pipeline to extract these relationships from the Open Access literature working with Europe PMC and developing machine learning and graph approaches for identifying novel and unexpected relationships.
The post will involve use of natural language processing to develop comprehensive entity recognition, testing and refinement of entity dictionaries, building a knowledge graph combining literature relationships with other evidence from the Open Targets Platform and machine learning to predict novel relationships including disease:target associations and drug repurposing opportunities.
- Participate in building an Open Targets Knowledge Graph
- Develop machine learning approaches to identify novel associations and other opportunities, and publish these.
- Build repertoire of training sets and gold standard for NLP for diverse entities
- Assess and feedback on performance of Europe PMC literature entity tagging including collating user feedback
- Contribute to implementation of graph-based approaches for the next generation Open Targets Platform
- PhD in Computer Science, Bioinformatics, Computational Biology, Data Science or related area
- Experience in Machine Learning or Natural Language Processing in a biological context
- Highly proficient in Python, Scala or equivalent programming language
- Must be able to communicate analysis and results clearly to a diverse audience
- Must be able to identify and clearly express limitations or pitfalls in potential approaches
You might also have
- Experience in an area related to drug discovery would be an advantage
- Experience with graphical-based approaches
- Familiarity with cloud computing environments
- Proficient with data analysis for instance in R
The position is embedded in the Open Targets Core Platform team. Extensive interaction with text mining and NLP experts in Europe PMC is required. Interaction with the full set of Open Targets Partners is expected.
Why join us
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 22 member states and two associate member states. 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.
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.
We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.
If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.
What else you need to know
To view a copy of the full job description please click here.
To apply please submit a covering letter and CV through our online system.
Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.
EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels.
Appointment will be based on merit alone.
Applications will close at 23:00 BST on the date listed above.