Data Harmonization Engineer - Hybrid, Growth & Impact

Capgemini Engineering; Lisboa; Hybrid; EUR 45,000 - 65,000; Full time

Benefits offered by this job

Health and life insurance

Referral program with bonuses fortal­-

Great office locations

Training and certifications programs

Hybrid work

Job summary

Capgemini Engineering is seeking a data engineer with a strong biomedical data background for our Lisbon team. You will design and run pipelines that map messy, multi-source data to canonical models and vocabularies, ensuring trust and readiness for analytics, knowledge graphs and AI use cases.

You will collaborate with scientists and engineers to translate needs into data requirements, validate quality, document rules, and mentor junior colleagues.

Qualifications

• MSc or PhD (or equivalent) in biology, biomedical sciences, bioengineering, genetics, neuroscience, bioinformatics, computational biology or related field.
• 3–5 years of experience in data engineering, bioinformatics or scientific data work with real biomedical datasets.
• Strong Python (pandas or similar) and SQL skills with pipelines built and maintained.
• Hands-on experience with data harmonization, mapping, vocabulary alignment and persistent identifiers.
• Experience with data quality assessment and validation frameworks, with code-based checks.
• Solid Git practice with meaningful commit history.
• Fluent English; Portuguese fluency is a plus.

Responsibilities

• Build and maintain Python and SQL pipelines for data manipulation, transformation and integration across multiple sources.
• Define and implement source-to-canonical mappings, persistent identifiers and vocabulary alignment.
• Design and automate data quality assessment: completeness, validity, consistency, uniqueness and provenance checks.
• Normalize entities (genes, diseases, phenotypes, compounds, tissues) against authoritative identifiers and ontologies.
• Work with scientists, data engineers and product teams to translate scientific needs into data requirements.
• Document mappings, modelling decisions and validation rules, and keep them in version control.
• Investigate and resolve data issues at the source, and communicate their impact.
• Mentor junior colleagues and review their code and mappings.

Skills

Python

SQL

Data harmonization

Data quality checks

Git

English

Portuguese

Education

MSc or PhD in biology / biomedical sciences / bioengineering or related field

Tools

Pandas

Airflow

Nextflow

Snakemake

Prefect

Docker

RDF/SPARQL knowledge (optional)

Job description

Capgemini Engineering is seeking a data engineer with a strong biomedical data background for our Lisbon team. You will design and run pipelines that map messy, multi-source data to canonical models and vocabularies, ensuring trust and readiness for analytics, knowledge graphs and AI use cases.

You will collaborate with scientists and engineers to translate needs into data requirements, validate quality, document rules, and mentor junior colleagues.