Data Engineer (System Specialist) 80-100%

The University of Basel is Switzerland's oldest university and is internationally recognized for its research excellence. With over 12,000 students and 5,000 researchers across seven faculties, the university fosters innovation across disciplines - from the humanities and social sciences to natural and life sciences.
 
As research becomes increasingly data-driven, the need for robust infrastructure and expert data support continues to grow. sciCORE, the University of Basel's Center for Scientific Computing, provides essential services for enabling cutting-edge, transdisciplinary research. Among its core offerings is the LabKey data management environment that integrates data and metadata from various university platforms such as genomics, proteomics, biobanking, and imaging, along with structured data from individual research projects. Although this service is available to a wide range of disciplines that work with structured data, its primary user base remains rooted in biomedical research. A strategic goal of the service is to enable interoperability between LabKey and national data infrastructures, such as the SPHN Semantic Data Framework.
 
We are seeking a Data Engineer (System Specialist) to join the Data Management Services (DMS) team within sciCORE. In this role, you will help develop and maintain the LabKey platform, supporting scalable and interoperable research data services. You will work closely with the LabKey service owner, sciCORE infrastructure specialists, and university researchers, combining data engineering and semantic data expertise to meet the evolving needs of data-intensive research across the university. Some projects will also involve collaborating with specialist groups such as the SPHN Semantic Data Harmonization Working Group. The position reports to the DMS Team Lead and offers a collaborative, service-driven work environment.
 

Your position

LabKey Service Development & Operations

  • Collaborate with the LabKey service owner and sciCORE domain experts to enhance and extend LabKey functionality.
  • Develop and deploy LabKey modules using Python, Java, JavaScript, and SQL, in particular tailored to biomedical research needs.
  • Integrate LabKey with related systems such as REDCap, LIMS, ELN, and institutional databases.
  • Establish and maintain automated data backup and restore processes to ensure data resilience and business continuity.
  • Collaborate with systems team to monitor system health, performance, and logs to ensure reliable operation and timely issue resolution.

Database Engineering & Support
  • Design, maintain, and optimize relational data models used in LabKey and associated systems.
  • Write performant SQL queries and procedures to support custom reports, API calls, and user data access.
  • Ensure data integrity, security, and access control in accordance with institutional policies.
  • Manage data import/export pipelines and support schema evolution as research projects progress.
  • Contribute to user-facing and internal documentation, code versioning, and reproducibility practices in data workflows.

Structured & Semantic Data Development & Support 
  • Guide users in applying ontologies and standards for semantic annotation (e.g., SNOMED CT, ICD-10, LOINC).
  • Develop and support linked data models (e.g., RDF, OWL) and tools that enable semantic interoperability. 
  • Promote use of metadata standards (e.g., FAIR principles) and support research metadata curation.
  • Act as a subject matter expert in semantic data integration across projects and research domains.
  • Provide training and support for research groups working with general structured and semantic biomedical data.
  • Engage with semantic expert groups and support projects with complex data management requirements (e.g. in SPHN context) as required.

Your profile

Essential

  • Master's degree in a domain related to information science and/or data semantics, with 5 or more years of work in academic research and/or work in data management at a higher education institution.
  • Experience with the LabKey platform, or the ability to learn and quickly contribute to complex web platforms for data management.
  • Experience in programming with scripting languages (e.g. Python, javascript, APls) in a Linux environment.
  • Strong SQL and data modeling skills; familiarity with PostgreSQL or SQL Server.
  • Extensive knowledge of semantic web technologies (e.g. RDF, SPARQL, GraphDB) and domain ontologies in the biomedical field.
  • Proven experience in supporting clinical research projects.
  • Service- and solution-oriented mindset with excellent collaboration and communication skills.
  • Proficiency in English as working language 

Desirable:
  • Experience working with data types and processes used in life sciences
  • German (oral and/or written)

We offer you

  • A collaborative, interdisciplinary environment at one of Switzerland's leading research institutions.
  • Direct impact on data infrastructure supporting critical research at the university.
  • Opportunities for professional development and further training.
  • Modern working conditions with flexibility for remote work.
  • A supportive team culture at sciCORE and within the Data Management Services team.
  • The initial contract is for 2 years, with the possibility to extend subject to funding and successful performance evaluation.

 Application / Contact
 
We look forward to receiving your complete application via the university's online application portal (see button below). Applications should include a curriculum vitae, a letter of motivation, and the names of three potential referees. Applications by email cannot be considered. For further information, please contact scicore@unibas.ch.
 
The position will remain open until filled.
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