Data Harmonization Engineer (Hybrid)

Capgemini Engineering; Fundão; Hybrid; EUR 42,000 - 62,000; Full time

Benefits offered by this job

Hybrid work

Health and life insurance

Training programs

Referral bonuses

Great office locations

Job summary

Capgemini Engineering in Portugal seeks a data engineer to design and run pipelines that map messy data to canonical models and identifiers, enabling analytics, knowledge graphs and AI use cases. You will turn raw data into trusted, queryable assets for scientists and data engineers.

You will build Python/SQL pipelines, implement mappings and vocabulary alignment, ensure data quality, document decisions, and mentor junior colleagues in a collaborative, hybrid work environment.

Qualifications

• MSc or PhD in biology, bioinformatics or related field.
• 3–5 years in data engineering, bioinformatics or scientific data work with real biomedical datasets.
• Strong Python (pandas) and SQL skills, with pipelines you built and maintained.
• Hands-on data harmonization & mapping, vocabulary alignment and persistent identifiers.
• Experience with data quality assessment and validation frameworks written as code.
• Solid Git practice with meaningful commit history.
• Biological reasoning about the data you handle.
• Fluent English and Portuguese language skills.

Responsibilities

• Build and maintain Python and SQL pipelines for data manipulation and integration.
• Define source-to-canonical mappings, persistent identifiers and vocabulary alignment.
• Automate data quality assessment: completeness, validity, consistency, provenance checks.
• Normalize entities against authoritative ontologies and identifiers.
• Collaborate with scientists and engineers to translate needs into data requirements.
• Document mappings and validation rules in version control.
• Mentor junior colleagues and review their code and mappings.

Skills

Python

SQL

Data harmonization

Vocabulary alignment

Git

Clear communication

Fluent English

Education

MSc or PhD in biology, bioinformatics or related field

Tools

Airflow

Prefect

Snakemake

Nextflow

Docker

Pandas

SHACL

Great Expectations

Pandera

SPARQL

LinkML

Job description

Capgemini Engineering in Portugal seeks a data engineer to design and run pipelines that map messy data to canonical models and identifiers, enabling analytics, knowledge graphs and AI use cases. You will turn raw data into trusted, queryable assets for scientists and data engineers.

You will build Python/SQL pipelines, implement mappings and vocabulary alignment, ensure data quality, document decisions, and mentor junior colleagues in a collaborative, hybrid work environment.