Sano Phd Student - Project Title: Biomedical Semantic Data Integration And Management

Universities and Institutes of Poland
October 09, 2022
Offerd Salary:Negotiation
Working address:N/A
Contract Type:Temporary
Working Time:Full time
Working type:N/A
Job Ref.:N/A
  • Organisation/Company: Sano Centre for Computational Personalized Medicine
  • Research Field: Computer science
  • Researcher Profile: First Stage Researcher (R1)
  • Application Deadline: 09/10/2022 21:00 - Europe/Athens
  • Location: Poland › Kraków
  • Type Of Contract: Temporary
  • Job Status: Full-time
  • Hours Per Week: 40
  • 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.


    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.

    Selection process

    Sano is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

    Do you recognize yourself in the job profile? Then we look forward to receiving your application.

    Applications in .pdf should include:

  • a cover letter.
  • a curriculum vitae.
  • Offer Requirements
  • Computer science: Master Degree or equivalent

  • ENGLISH: Excellent


    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.
  • Contact Information
  • Organisation/Company: Sano Centre for Computational Personalized Medicine
  • Organisation Type: International / Intergovernmental Organisation
  • Website: https: //
  • E-Mail:
  • Country: Poland
  • City: Kraków
  • State/Province: Malopolska
  • Postal Code: 30054
  • Street: Czarnowiejska 36
  • From this employer

    Recent blogs

    Recent news