Sano Postdoc - Project title: Biomedical Semantic Data Integration and Management

Location Krakow
Employment type Full-time
Region / State / Province małopolskie
About job:

Sano Postdoc

Project title: Biomedical Semantic Data Integration and Management

Publication date: 9.09.2022

Closing date: 09.10.2022

Level of education: PhD

Hours: 40 hours per week

Salary indication: up to 14000 PLN gross monthly


Sano: Dr. Ahmed Abdeen Hamed (Clinical Data Science collab between PhD student and postdoc)

Project period: October/November 2022

The position is for Sano's Clinical Data Science team. Our group develops a new generation of semantically integrated databases for clinical and biomedical. Our system will build on recent Big Data workflow technologies to integrate using a multitude of very large data sets, including text mining results, mutation databases, internal and external -omics high-throughput sets, ontologies, and clinical data.  

The project sets out to provide an ultimately fine-grained implementation of parsing, extracting, integrating, and querying classes of ontologies which can be processed efficiently and have other desirable computational properties. The overall aim of this approach is to enable ontology engineers to design and customize ontologies that strike an ideal balance between the knowledge provided and efficient processing, in this way developing ontology-mediated querying to its full potential.

The position is especially adequate for Postdocs, PhD students or engineers who want to learn about, apply and further develop workflow technologies for scalable data integration in the exciting field of clinical data science and analytics. You will contribute to the ambition of Sano's Clinical Data Science team to be nationally and internationally recognized for its strengths in clinical data science in general and biomedical data analytics, in particular.

What are you going to do?

You are expected to:

  • do original research under the direction of one of Research Group Leaders;
  • publish your work in peer-review journals and present during national and international conferences;
  • co-mentor junior scientists – PhD students and MSc students.
What do we require?

Required background and skills of the candidate:

  • Recent or pending PhD in relevant field, preferably computer science;
  • at least one first-author research publication in a peer-reviewed scientific journal, top conference or currently in press;
  • Expertise in working with the Biomedical ontologies (OWL/RDF/XML/JSON/OBO) formats;
  • Demonstrated experience with semantic annotations and semantic networks;
  • Developing microservices-based APIs;
  • Proficiency programming for databases (MySQL, PostgreSQL, K-V databases);
  • Knowledge of Graph Databases (Neo4J, RDF DB);
  • excellent written and oral English communication skills.
Our offer

We offer a fixed term contract for 40 hours per week. This will be supported by an educational plan that includes attendance of courses and (international) meetings. The contract will include opportunities to participate in teaching and supervision of undergraduate and master students.

The salary, depending on relevant experience before the beginning of the employment contract, will be up to 14000 PLN gross per month, based on a full-time contract (40 hours a week) for the duration of up to 2 years with private medical care and a sports card.

Sano offers excellent opportunities for study and development, an access to many international conferences on computational medicine and a possibility to grow in a scientific society
Last modified Friday, September 9, 2022