Senior Data Modeller

Capgemini Engineering; Porto; Hybrid; EUR 70,000 - 110,000; Full time

Benefits offered by this job

Hybrid work

Health and life insurance

Referral program with bonuses

Job summary

Capgemini seeks a senior modeller to lead data harmonization and FAIR data product initiatives across biomedical data assets.

You will translate complex scientific requirements into canonical models, set ontology Governance, identifiers and provenance standards, and mentor junior modelers while collaborating with biology, data engineering and platform teams.

Qualifications

• Advanced degree or equivalent in biology or related field.
• 6+ years in scientific data modelling, data harmonization or knowledge engineering.
• Experience with LinkML or equivalent schema framework.
• Proven data harmonization, mappings, provenance and identifiers.

Responsibilities

• Lead modelling strategy across data harmonization, pipeline validation, knowledge graph and FAIR data product requirements.
• Translate ambiguous requirements into canonical data models and document ontology decisions.
• Model biomedical entities and relationships, including genes, diseases, phenotypes, and more.
• Define persistent identifiers and provenance fields across data assets.
• Drive schema reviews, versioning and releases in GitHub with changelogs and impact assessment.
• Mentor junior and mid-level modelers.

Skills

Modelling strategy

Data harmonization

Knowledge graph

Ontology governance

Python

SQL

GitHub

Stakeholder management

English fluency

Education

MSc/PhD in biology or related field

Tools

LinkML

GitHub workflows

Docker

Job description

YOUR ROLE

You will lead a modelling strategy for scientific data harmonization work. This work aims to strengthen mechanistic understanding of disease and make integrated FAIR data products available to R&D scientists for rapid query and decision-making. You turn ambiguous scientific requirements into clear canonical models, make and document ontology decisions, and set the standards for identifiers, provenance and schema governance across data assets.

• Lead modelling strategy across data harmonization, pipeline validation, knowledge graph and FAIR data product requirements
• Translate ambiguous scientific requirements into clear conceptual, logical and canonical data models
• Model biomedical entities and relationships including genes, targets, diseases, indications, phenotypes, mechanisms, biomarkers, tissues, cell types, assay modalities, evidence, provenance and causal relationships
• Make ontology reuse, extension and mapping decisions, with documented rationale
• Define persistent identifiers and consistent provenance fields across data assets
• Drive schema review, approval, versioning and publication processes in GitHub, including changelogs, tagged releases and downstream impact assessment
• Define validation rules and data quality checks for ontology terms, ranges, required fields, ID and label consistency, cross-field consistency and provenance completeness
• Identify modelling risks early: metadata gaps, ontology conflicts, source data quality issues, lineage gaps and downstream compatibility problems
• Design modular, reusable and future-proof models aligned to FAIR principles and enterprise standards
• Work with scientific knowledge engineering, biology SMEs, data engineering, knowledge graph engineering, product management, data stewards and platform teams
• Mentor junior and mid-level modelers

YOUR PROFILE

• MSc or PhD (or equivalent professional experience) in biology, biomedical sciences, bioengineering, genetics, neuroscience, bioinformatics, computational biology or a related field
• More than 6 years of experience in scientific or biomedical data modelling, data harmonization or knowledge engineering, with senior ownership
• Strong conceptual, logical and canonical modelling experience for complex biomedical or scientific domains
• Practical, in-depth experience with LinkML or an equivalent schema framework: classes, slots, ranges, identifiers, required fields, constraints, cardinality, descriptions and ontology bindings
• Strong data harmonization experience: source-to-canonical mapping, controlled vocabulary alignment, persistent identifiers, lineage and provenance
• Proven experience defining validation rules and data quality checks: ontology term validity, ranges, required fields, ID and label consistency, cross-field consistency and provenance completeness
• Strong understanding of FAIR principles, metadata standards, provenance and schema versioning
• Strong command of biomedical ontologies and vocabularies such as HGNC, Ensembl, UniProt, MONDO, Disease Ontology, HPO, EFO, UBERON, Cell Ontology, Gene Ontology, Reactome, KEGG, ChEBI, OBI, LOINC, UCUM, ECO, SEPIO, Relation Ontology and PATO
• Experience managing the schema lifecycle with GitHub-based repositories, semantic versioning, changelogs, data dictionaries and metadata catalogues
• Experience designing models that support pipelines, APIs, knowledge graphs, FAIR data products and analytical workflows
• Solid Python and a working command of SQL, used for validation, mapping checks and exploration of real biomedical datasets
• A public or shareable repository (GitHub, GitLab or similar) demonstrating schema and governance work. Please include the link in your application
• Excellent stakeholder management and communication;
• Fluent English

Preferred Qualifications

• Semantic modelling technologies: RDF, OWL, JSON-LD, SHACL, ShEx and SPARQL; knowledge graph modelling
• Schema or model registry, data catalogue and metadata registry tooling
• Lineage and provenance modelling, and FAIR metadata assessment
• Query-based validation using SQL or Python and notebooks for model conformance, ontology mapping or data quality checks
• Agentic AI or LLM-assisted mapping and curation, with robust validation
• Experience in pharmaceutical R&D or another regulated research environment
• Cloud platforms, Docker and workflow orchestration
• Applied machine learning and/or broad data science
• Experience mentoring or leading a small technical team
• 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
• Portuguese fluency

What You´ll Love About Working Here

• Join a multicultural and inclusive team environment.
• Enjoy a supportive atmosphere promoting work life balance.
• 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.
• Access valuable training and certifications in cutting edge technologies.
• Engage in exciting national and international projects.
• 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.