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Data Management Specialist (80-100%)

University of Basel
Basel, Switzerland
Closing date
Sep 28, 2022

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The University of Basel is the oldest university in Switzerland, it counts over 12'000 students and 4'300 researchers in 7 faculties active in domains from humanities, economy to natural sciences.
In this context, sciCORE is the center of competence in scientific computing, maintaining an advanced computing infrastructure for active research and the associated services (including data management and scientific support). sciCORE is in particular developing and maintaining a secure IT infrastructure, sciCOREmed, suitable for biomedical research with data from hospitals.

sciCOREmed is co-funded by the University of Basel and by the national project BioMedIT, managed by SIB - Swiss Institute of Bioinformatics, in support of the initiative Swiss Personalized Health Network ( SPHN ). In the current phase of implementation of BioMedIT services (2021-2024), Swiss university hospitals are ramping up the adoption of standardized data formats and exchange protocols to make patient data more easily available for research. As an university research platform, we are seeking to reinforce our support capacity with such advanced data management technologies and concepts, bridging the gap between data managers in hospitals and data scientists in academia.

As our new collaborator you will support and train researchers in using the data technologies adopted in the national initiative. The position will require flexibility and curiosity, a good sense of organization and a support-oriented mindset. You will be able to support several projects simultaneously, addressing at different levels all aspects of data management of biomedical data: data storage in graph database, annotation of data using semantic technologies, access control, de-identification techniques, data sharing through access-controlled repositories, patient consent tracking. A strong focus of the SPHN initiative is in promoting the adoption of RDF (Resource Description Framework) for data exchanges.

As part of an agile and cooperative work environment you will be integrated in the local team of system, data management, and data analysis specialists at sciCORE, and work closely with data managers at other sites of the BioMedIT network (ETH, SIB Lausanne) and with the semantic experts of the Personalized Health Informatics Group of SIB in Basel.

The position is bound to the funding of BioMedIT project and is available immediately.
Duration of contract: three years with possibility of extension depending on availability of funds.

Your position

As our new collaborator, you will:
  • Be the point of contact for data-management support according to the FAIR principles in projects using hospital data, in particular in the sciCOREmed environment
  • Maintain expert knowledge in the data management technologies promoted by the SPHN/BioMedIT initiative (RDF, SPARQL)
  • Provide consulting and technical support with the tools offered as a service locally (GraphDB, WebProtégé, LabKey, XNAT), and in the BioMedIT network (OpenBIS, Kheops)
  • Be the local expert for semantic resources, in particular with Snomed CT, LOINC, ICD family, MeSH and related
  • Prepare guidelines and how-tos to help researchers help themselves with out semantic framework
  • Provide technical support for data exchanges between hospitals and research projects (data quality and semantic aspects)
  • Contribute to the technical developments in the BioMedIT network
  • Collaborate with sciCORE scientific IT specialists to develop/adapt data management solutions

Your profile

  • PhD or Masters with 3 or more years of work in academic research
  • Proven experience of work with semantic data management tools (RDF, GraphDB, biomedical ontologies, preferably with SNOMED CT, ICD-*, LOINC,)
  • Experience in programming with scripting languages (Python, javascript, APIs) in Linux environment
  • Motivated by work in academic-research context (close to researchers)
  • Proactive, service-oriented and collaborative spirit of mind
  • Fluent in English (oral and written) as working language
  • Hands-on experience with additional database technologies (NoSQL, SQL databases)
  • Prior experience in research support role
  • Experience with data management in hospital context (with private and sensitive personal data)
  • German (oral and/or written)

We offer you

  • A key position in support of research at university
  • The opportunity to work in a friendly local and national network of domain-specialists
  • A chance to develop creative-yet-robust solutions to practical data management challenges
  • The opportunity to work with cutting-edge scientific computing and data management technologies
  • The social benefits of the University of Basel

pplication / Contact

If you are interested in this challenging and highly interesting position, please submit your application including CV, letter of motivation and references through our online portal. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered. For further information regarding the position, please contact

The position will remain open until filled. Start date is as soon as possible.
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