Knowledge Graph Engineer (Life Sciences)

Capgemini; Évora; Hybrid; EUR 32,000 - 52,000; Full time

Benefits offered by this job

Hybrid work

Training programs

Health and life insurance

Referral program with bonuses

Great office locations

Job summary

Capgemini Engineering is seeking a skilled data and semantic technologies engineer to build and maintain a scientific knowledge graph. You will convert biological concepts into RDF models, develop Python pipelines, and ensure traceability to sources and evidence for analytics and AI applications.

You will work with scientists to resolve terminology, validate mappings to ontologies like GO, MONDO and HPO, and implement quality checks. Hybrid work and international opportunities are offered.

Qualifications

• MSc or PhD in biology, biomedical sciences, bioengineering, genetics, neuroscience, bioinformatics or related field.
• 3–5 years in data engineering, software engineering, semantic technologies or scientific data work.
• Strong Python and data manipulation skills with SQL knowledge.
• Experience with RDF modelling (OWL, SHACL) and SPARQL; provenance and quality emphasis.
• Knowledge of ontologies, taxonomies and knowledge graphs; source-to-ontology mapping.

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).
• Collaborate with scientists and ontology specialists to resolve terminology and data-quality questions.
• Document mapping rules, modelling decisions and validation rules.
• Support integration of graph assets into downstream data, analytics and AI solutions.

Skills

Python

SPARQL

RDF/OWL

SQL

Data manipulation

Git

Communication

English fluency

Education

MSc/PhD in biology or related field

Tools

OWL

SHACL

RDFLib

Neo4j/GraphDB

Job description

CAPGEMINI ENGINEERINGAt 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 ROLEYou 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 responsibilitiesDesign RDF-based data models and reusable semantic structures for genes, proteins, diseases, phenotypes, compounds and experimentsMap structured and unstructured data to controlled vocabularies and ontologiesDevelop Python pipelines for data transformation, entity resolution and RDF generationDefine and validate identifiers, relationships, provenance and evidenceWrite SPARQL queries to explore, test and analyze knowledge graphsImplement automated semantic quality checks and mapping validation (SHACL or equivalent)Collaborate with scientists and ontology specialists to resolve terminology, modelling and data-quality questionsDocument mapping rules, modelling decisions and validation rulesSupport the integration of graph assets into downstream data, analytics and AI solutionsYOUR PROFILEMSc or PhD (or equivalent professional experience) in biology, biomedical sciences, bioengineering, genetics, neuroscience, bioinformatics, computational biology or a related field3 to 5 years of experience in data engineering, software engineering, semantic technologies or scientific data workStrong Python and data manipulation skills, and a working command of SQLPractical RDF modelling (subject, predicate, object) and hands-on experience with OWL, SPARQL and SHACL, plus RDFS or triple storesExperience designing source-to-ontology mappings or integrating multiple scientific data sourcesPractical experience using or developing ontologies, taxonomies, controlled vocabulary or knowledge graphsUnderstanding of provenance, metadata, data quality and schema validationExperience with biological or biomedical datasetsGit and modern software development practicesClear communication with scientific and technical stakeholdersFluent EnglishPreferred qualificationsHands-on experience with Gene Ontology, MONDO, HPO, EFO, UBERON, ChEBI or other OBO Foundry ontologiesSemantic-web libraries such as RDFLib or OWLReady2Entity linking, terminology mapping or controlled vocabulary managementRDF-star, named graphs or property graph modelling (Neo4j, GraphDB)Knowledge of FAIR principles, scientific metadata governance and LinkMLAgentic AI experience & LLM-based agents, retrieval-augmented generation, information extraction or LLM-assisted mapping, with validation of the outputExposure to graph analytics, semantic similarity, machine learning or generative AIAPIs, Docker, cloud platforms, workflow orchestration and automated data pipelinesExperience in pharmaceutical & healthcare or another regulated environmentPortuguese fluencyWhat we look forScientific curiosity paired with engineering disciplineCritical thinking and attention to data provenance and qualityComfort with ambiguity, and the ability to move between scientific meaning and technical implementationAn impact-driven mindset in a fast-paced environmentWHAT YOU'LL LOVE ABOUT WORKING HEREJoin 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 CAPGEMINICapgemini 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.