Data Harmonization Engineer — Hybrid, Growth & AI-Ready

Capgemini Engineering; Évora; Hybrid; EUR 55,000 - 85,000; Full time

Benefits offered by this job

Hybrid work

Health and life insurance

Training and certifications programs

Referral program with bonuses

Job summary

Capgemini Engineering is seeking a data engineer/scientist to design and run Python and SQL pipelines that map messy data to canonical models and vocabularies. You will ensure trustworthiness for analytics, knowledge graphs and AI use cases, joining scientists and engineers to transform raw data into queryable, reliable datasets.

The role requires 3–5 years in data engineering or bioinformatics, plus strong Python and SQL skills, data quality checks, and experience with ontologies and

Qualifications

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

Responsibilities

• Build and maintain Python and SQL pipelines for data manipulation and integration across sources.
• Define source-to-canonical mappings and persistent identifiers.
• Design automated data quality checks for completeness, validity, consistency and provenance.
• Normalize biological entities against authoritative ontologies.
• Translate scientific needs into data requirements with colleagues and teams.
• Document mappings and validation rules and keep in version control.
• Investigate data issues at the source and communicate impact.
• Mentor junior colleagues and review code and mappings.

Skills

Python

SQL

Data harmonization

Vocabulary alignment

Data quality assessment

Git

Scientific communication

Fluent English

Education

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

Tools

Python

SQL

Airflow

Prefect

Snakemake

Nextflow

Docker

Job description

Capgemini Engineering is seeking a data engineer/scientist to design and run Python and SQL pipelines that map messy data to canonical models and vocabularies. You will ensure trustworthiness for analytics, knowledge graphs and AI use cases, joining scientists and engineers to transform raw data into queryable, reliable datasets.

The role requires 3–5 years in data engineering or bioinformatics, plus strong Python and SQL skills, data quality checks, and experience with ontologies and