Data Harmonization Engineer — Hybrid Work & Growth

Capgemini Engineering; Porto; Hybrid; EUR 42,000 - 66,000; Full time

Benefits offered by this job

Health and life insurance

Hybrid work

Training and certifications

Referral program with bonuses

Great office locations

Job summary

CAPGEMINI ENGINEERING in Porto seeks a data engineer to design and run Python and SQL pipelines, map messy multi-source data to canonical models, and ensure data quality for analytics, knowledge graphs and AI use cases.

You will work with scientists and engineers to translate scientific needs into data requirements, document mappings, and mentor junior colleagues while contributing to data harmonization and vocabularies with persistent identifiers.

Qualifications

• MSc or PhD (or equivalent) in biology, biomedical sciences, bioengineering, genetics, neuroscience, bioinformatics 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 you built and maintained.
• Hands-on experience with data harmonization & mapping, vocabulary alignment and persistent identifiers.
• Experience with data quality assessment and validation frameworks, with checks written as code.
• Solid Git practice & branches, pull requests, meaningful commit history.
• Biological reasoning about the data you handle (genes, variants, diseases, phenotypes, assays).
• Clear communication with scientific and technical stakeholders.
• Fluent English.
• Preferred qualifications: extensive biomedical ontologies, agentic AI, validation frameworks, workflow orchestration, cloud platforms, FAIR/RDF/SPARQL, ML, regulated environments, Portuguese fluency.

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 (pandas) & SQL

Data harmonization & mapping

Data quality assessment

Git version control

Biology / bioinformatics background

Communication with stakeholders

Fluent English

Team mentoring

Education

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

Tools

Airflow

Snakemake

Nextflow

Docker

SQL

Git

Schema modelling (LinkML)

Job description

CAPGEMINI ENGINEERING in Porto seeks a data engineer to design and run Python and SQL pipelines, map messy multi-source data to canonical models, and ensure data quality for analytics, knowledge graphs and AI use cases.

You will work with scientists and engineers to translate scientific needs into data requirements, document mappings, and mentor junior colleagues while contributing to data harmonization and vocabularies with persistent identifiers.