Sano PhD Student - Project title: Biomedical Semantic Data Integration and Management

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

Sano PhD Student

Project title: Biomedical Semantic Data Integration and Management

Publication date: 9.09.2022

Closing date: 09.10.2022

Level of education: Master's degree

Hours: 40 hours per week

Salary indication: up to 8000 PLN gross monthly


Sano: dr. Ahmed Abdeen Hamed (Clinical Data Science Research Group Leader)

Project start: 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 in this field under the direction of the Project’s Principal Investigator.
  • Participate in seminars by internal and external speakers as well as journal clubs and group activities.
  • Collaborate with other PhD candidates, postdoctoral researchers, and other Sano employees.
What do we require?

Required background and skills of the candidate:

  • Master's degree (completed or near completion) in a relevant discipline, such as data; science, mathematics, biostatistics, computational biology, computational chemistry;
  • Proficiency in Python, Java, and/or Julia programming;
  • 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);
  • Prior research experience in academia or industry is a plus;
  • A great deal of interest in pursuing computational medicine research.
Our offer

We offer a fixed term contract for 40 hours per week for the duration of 4 years. 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 8000 PLN gross per month, based on a full-time contract (40 hours a week) for the duration of 4 years with private medical care and a sports card.

This PhD will be a collaboration between Sano and a degree awarding body. The student will be based in Poland, operating in conjunction with the Cyfronet supercomputing centre hosted by AGH.

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, December 2, 2022