Life Sciences Data Harmonization Engineer

Capgemini; Évora, Lisboa, Fundão, Vila Nova de Gaia; Hybrid; EUR 42,000 - 66,000; Full time

Benefits offered by this job

Hybrid work

Health and life insurance

Referral program with bonuses

Career growth programs

Job summary

Capgemini Engineering in Portugal seeks a Data Harmonization Engineer (Life Sciences) to design and run pipelines that map messy, multi-source data to canonical models and vocabularies. You will help ensure data quality, provenance and readiness for analytics, knowledge graphs and AI use cases.

You collaborate with scientists and engineers to translate scientific needs into data requirements, document mappings and validation rules, and mentor junior colleagues while maintaining code in version

Qualifications

• MSc/PhD in biology or related field.
• 3–5 years in data engineering, bioinformatics or scientific data work.
• Experience with biomedical datasets and data harmonization.
• Strong Python and SQL skills with pipeline development.

Responsibilities

• Design and run Python/SQL pipelines for data manipulation and integration.
• Define source-to-canonical mappings and persistent identifiers.
• Implement data quality checks and provenance validation in code.
• Normalize entities against authoritative ontologies and vocabularies.
• Collaborate with scientists and engineers to translate needs into data requirements.
• Document mappings and validation rules and maintain version control.

Skills

Python

SQL

Data mapping

Data quality

Git

Pandas

Education

MSc/PhD in biology or related field

Tools

Airflow

Prefect

Snakemake

Nextflow

Docker

LinkML

Job description

Capgemini Engineering in Portugal seeks a Data Harmonization Engineer (Life Sciences) to design and run pipelines that map messy, multi-source data to canonical models and vocabularies. You will help ensure data quality, provenance and readiness for analytics, knowledge graphs and AI use cases.

You collaborate with scientists and engineers to translate scientific needs into data requirements, document mappings and validation rules, and mentor junior colleagues while maintaining code in version