The SIB Swiss Institute of Bioinformatics is an internationally recognized non-profit organization, dedicated to biological and biomedical data science. Its data scientists are passionate about creating knowledge and solving complex questions in many fields, from biodiversity and evolution to medicine. They provide essential databases and software platforms as well as bioinformatics expertise and services to academic, clinical, and industry groups. SIB federates the Swiss bioinformatics community of some 900 scientists, encouraging collaboration and knowledge sharing. The Institute contributes to keeping Switzerland at the forefront of innovation by fostering progress in biological research and enhancing health.
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Employer
SIB Swiss Institute of Bioinformatics
Work Location
Basel, Switzerland
Employment fraction
80% - 100%
Type of contract
permanent
The Swiss Personalized Health Network (SPHN) is a national network mandated by the State Secretariat for Education, Research and Innovation (SERI) to enable the secure reuse of health data for research and innovation. Its mission is to ensure that clinical information collected across Swiss hospitals can be made FAIR (Findable, Accessible, Interoperable, and Reusable) and comparable across institutions.
SPHN fosters interoperability at two complementary levels:
- Semantic interoperability through common data models, ontologies, and terminologies, enabling health data to be linked, queried, and understood consistently across institutions.
- Computational interoperability through BioMedIT, a secure federated IT infrastructure connecting Swiss hospitals and research institutions, providing trusted environments for privacy-preserving data transfer, storage, and analysis.
To strengthen its semantic layer, SPHN is seeking a Senior Software Developer with strong expertise in Semantic Web technologies, particularly SPARQL, and a solid understanding of data pipeline infrastructures and architectures. The successful candidate will contribute to the design and implementation of solutions that put semantic interoperability into practice across the Swiss health data ecosystem.
- Contribute to the design and implementation of ontologies, data models, and APIs supporting semantic interoperability of health data.
- Develop and maintain semantic data services, with a focus on SPARQL query optimization and integration with RDF triple stores (e.g., GraphDB, Virtuoso).
- Build tools and workflows that support the alignment of health datasets with international medical informatics standards (FHIR, SNOMED CT, LOINC, HealthDCAT).
- Collaborate with clinicians, researchers, and IT specialists to translate semantic interoperability requirements into robust technical solutions.
- Lead the development and on-premises implementation of ETLs and software such as the SPHN Connector and Einstein, enabling secure and standardized data exploration across Switzerland.
- Minimum of a Master's degree in Computer Science, Software Engineering, Bioinformatics or related field and five years experience in software development or data infrastructure projects, or equivalent and additional work experience in a relevant field.
- Strong expertise in Semantic Web technologies (RDF, SPARQL, SHACL).
- Hands-on experience with triple stores (e.g. Virtuoso, GraphDB, Jena Fuseki, Stardog).
- Solid Python development skills, ideally including frameworks such as FastAPI or Django/Flask, and familiarity with data processing libraries.
- Good understanding of software architectures, ideally with exposure to cloud and HPC infrastructures; experience with OpenStack.
- Experience with agile development, version control (Git), and CI/CD pipelines for automated testing and deployment.
- Familiarity with medical informatics standards (HL7 FHIR, SNOMED CT, LOINC) is an advantage.
- Practical experience with containerization technologies (Docker, Singularity, or Kubernetes) is an advantage.
- Self-starter with an ability to work independently as well as in a group.
- Strong problem-solving and analytical skills, detail-oriented.
- Ability to work in an agile environment.
- Excellent communication and teamwork capabilities.
- Proficiency in English both oral and writing. French, German or Italian is a plus.
- Eager to learn new technologies.