Knowledge Graph Engineer (Life Sciences)

CAPGEMINI ENGINEERING
At Capgemini Engineering, the world leader in engineering services, we bring together a global team of engineers, scientists, and architects to help the world’s most innovative companies unleash their potential. From autonomous cars to life-saving robots, our digital and software technology experts think outside the box as they provide unique R&D and engineering services across all industries. Join us for a career full of opportunities. Where you can make a difference. Where no two days are the same.
YOUR ROLE
You will build and maintain the scientific knowledge graph content that will be used to answer scientific questions. You turn biological concepts into ontology-aligned RDF models, write the Python pipelines that generate them, and keep every assertion traceable to its source and evidence. You bridge scientific meaning and technical delivery, so that graph assets are accurate, governed and usable by analytics and AI applications.
Key responsibilities
Design RDF-based data models and reusable semantic structures for genes, proteins, diseases, phenotypes, compounds and experiments
Map structured and unstructured data to controlled vocabularies and ontologies
Develop Python pipelines for data transformation, entity resolution and RDF generation
Define and validate identifiers, relationships, provenance and evidence
Write SPARQL queries to explore, test and analyze knowledge graphs
Implement automated semantic quality checks and mapping validation (SHACL or equivalent)
Collaborate with scientists and ontology specialists to resolve terminology, modelling and data-quality questions
Document mapping rules, modelling decisions and validation rules
Support the integration of graph assets into downstream data, analytics and AI solutions
YOUR PROFILE
MSc or PhD (or equivalent professional experience) in biology, biomedical sciences, bioengineering, genetics, neuroscience, bioinformatics, computational biology or a related field
3 to 5 years of experience in data engineering, software engineering, semantic technologies or scientific data work
Strong Python and data manipulation skills, and a working command of SQL
Practical RDF modelling (subject, predicate, object) and hands-on experience with OWL, SPARQL and SHACL, plus RDFS or triple stores
Experience designing source-to-ontology mappings or integrating multiple scientific data sources
Practical experience using or developing ontologies, taxonomies, controlled vocabulary or knowledge graphs
Understanding of provenance, metadata, data quality and schema validation
Experience with biological or biomedical datasets
Git and modern software development practices
Clear communication with scientific and technical stakeholders
Fluent English
Preferred qualifications
Hands-on experience with Gene Ontology, MONDO, HPO, EFO, UBERON, ChEBI or other OBO Foundry ontologies
Semantic-web libraries such as RDFLib or OWLReady2
Entity linking, terminology mapping or controlled vocabulary management
RDF-star, named graphs or property graph modelling (Neo4j, GraphDB)
Knowledge of FAIR principles, scientific metadata governance and LinkML
Agentic AI experience & LLM-based agents, retrieval-augmented generation, information extraction or LLM-assisted mapping, with validation of the output
Exposure to graph analytics, semantic similarity, machine learning or generative AI
APIs, Docker, cloud platforms, workflow orchestration and automated data pipelines
Experience in pharmaceutical & healthcare or another regulated environment
Portuguese fluency
What we look for
Scientific curiosity paired with engineering discipline
Critical thinking and attention to data provenance and quality
Comfort with ambiguity, and the ability to move between scientific meaning and technical implementation
An impact-driven mindset in a fast-paced environment
WHAT YOU'LL LOVE ABOUT WORKING HERE
Join a multicultural and inclusive team environment.
Enjoy a supportive atmosphere promoting work-life balance.
Engage in exciting national and international projects.
Hybrid work.
Your career growth is central to our mission. Our array of career growth programs and diverse professionals are crafted to support you in exploring a world of opportunities.
Training and certifications programs.
Health and life insurance.
Referral program with bonuses for talent recommendations.
Great office locations.
ABOUT CAPGEMINI
Capgemini is the business transformation partner for enterprises in the age of AI. We help organizations imagine and build an intelligent, sustainable future, combining AI, technology and human ingenuity to transform how they operate, innovate and grow. With unique end-to-end capabilities spanning strategy, technology, engineering and intelligent operations, we bring together deep industry expertise and market-leading capabilities in AI, cloud and data to turn ambition into measurable business outcomes at scale. Supported by a robust ecosystem of partners and nearly 60 years of expertise, Capgemini is a responsible and diverse global organization of over 410,000 team members in more than 50 countries.