Scientific Developer (Chemical Biology Resources)

About the team/job

Safety and toxicology concerns remain one of the most persistent challenges in drug discovery. This is an exciting opportunity to join a multi-disciplinary team on a project to develop a comprehensive open source side effect resource for the scientific and pharmaceutical community, and provide structured and standardised training sets for AI/ML applications to improve early identification of safety liabilities.      

You will harness modern machine learning techniques to extract data from a range of relevant resources, such as clinical trials, publications and drug labels. You will work closely with team members to ensure development of automated pipelines and effective integration into the ChEMBL database (https://www.ebi.ac.uk/chembl/) and Open Targets Platform (https://platform.opentargets.org/), to assist users in the selection of safe and efficacious drug targets.

The Chemical Biology Resources team at EMBL-EBI provides world-leading chemogenomics resources to the scientific community including ChEMBL, a database of quantitative small-molecule bioactivity data curated primarily from the scientific literature widely used to support drug discovery projects in industry and academia. The Safety 2.0 project is funded by Open Targets, a unique public-private partnership working to deliver experimental data and informatics resources that enable scientists to make more informed decisions about target selection for developing safer and more effective drugs. You will interact with safety scientists from Open Targets pharmaceutical partners MSD, Genentech, GSK, Pfizer, and Sanofi to understand requirements and how to help contribute to evaluating drug and target safety. You will be embedded at the world-leading EMBL-EBI, and will work collaboratively across the Chemical Biology Resources and Open Targets groups, benefitting from a range of multi-disciplinary expertise and technologies.  

Your role

We are looking for an enthusiastic and talented scientific developer in the area of cheminformatics or bioinformatics with an interest in biomedical knowledge extraction to join the Open Targets Safety 2.0 project. You should enjoy addressing challenges in knowledge extraction and data standardisation, and want to contribute to open source code and resources. 

The project will develop a new side effect resource for drug discovery based on the extraction of side effect data from a range of documents. Your role will focus on developing and implementing machine learning and data processing pipelines for the extraction of safety data. The position provides a real opportunity to make a significant impact on a critical problem in drug discovery for the many users of the Open Targets Platform and ChEMBL.

This position will be situated within the Chemical Biology Resources team (https://www.ebi.ac.uk/about/teams/chemical-biology-resources/). You will work closely with other Safety 2.0 project team members to ensure effective delivery of workpackages, and collaboratively with the Chemical Biology Resources team and Open Targets Core teams to ensure effective integration and longevity of pipelines and resources.

Key responsibilities

• To work closely as part of a team across Chemical Biology Resources and Open Targets to deliver a drug side-effect resource

• Develop machine learning pipelines for extracting drug side effects from drug labels, clinical trials, publications and other documents, and mapping to biomedical ontologies

• Integrate project workflows with existing infrastructures in the EBI Chemical Biology Resources and Open Targets teams

• Assist with data curation to prepare clean and reliable training sets

• Collaborate with the Open Targets pharmaceutical partners to assess, prioritise, validate and refine the developed methods

• Disseminate the outcomes of the project to the scientific community and stakeholders through presentations and publications

You have

• PhD or equivalent experience in cheminformatics, bioinformatics or another relevant scientific discipline

• Proficiency in Python

• Excellent attention to detail and problem-solving skills

• Strong communication skills, both presentations and verbal

• An interest in contributing to a global resource which will have a positive impact on research and development of safe drugs

You might also have

• Experience with the application of NLP methods or LLMs to biomedical domain

• Experience with document and text preprocessing, cleaning and transformation techniques including mapping to ontologies

• Experience with data structures, data models and databases

• Experience in Safety/toxicology in industrial or academic research

• Experience with version control, and software testing

Contract length: 2 years

Salary: Grade 5 or 6, monthly salary from £3,452 or £3,861 after tax, plus generous benefits and financial allowances based on family circumstances. Excluding persona pension and insurance contributions.

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.  Watch this video to see how EMBL-EBI makes an impact.

Enjoy lots of benefits:

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances

• Flexible working arrangements - including hybrid working patterns 

• 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 public 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 detailed information please visit our employee benefits page here. 

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.  

• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.

• Diversity and inclusion: At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.

• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date