Karolinska Institutet, Institutionen för neurovetenskap, INCF

The Department of Neuroscience includes several research groups working on different aspects of nervous system function, both under normal conditions and in various disease states. Research projects include a broad range of studies on the molecular and cellular levels, networks of neurons, and the organization of the nervous system as a whole. The Department has a flat organization with 40 researchers, of which 24 are full professors and 65 PhD students.

Teaching represents a fundamental activity at the Department, which participates in several undergraduate courses and postgraduate education programs. Each year approximately 15 students receive their PhD from our Department and many of our graduates have gone onto distinguished careers in the academic or private sector.

Join the INCF Secretariat at the Karolinska Institute in Stockholm, Sweden.

The International Neuroinformatics Coordinating Facility (INCF) is an international organization launched in 2005, following a proposal from the Global Science Forum of the OECD to establish international coordination and collaborative informatics – and currently has 18 member countries across North America, Europe, Australia and Asia. INCF establishes and operates scientific programs to develop standards for neuroscience data sharing, analysis, modeling and simulation while coordinating an informatics infrastructure designed to enable the integration of neuroscience data and knowledge world worldwide and catalyze insights into brain function in health and disease.

Key Functions:

INCF is looking for an experienced ontologist to lead a 6 month project to develop ontologies that will support database integration into KnowledgeSpace (knowledge-space.org), a data-driven encyclopedia for neuroscience which links brain concepts to data, models, and literature, and map KnowledgeSpace ontologies to the Neuroscience Information Framework (NIF) Standard Ontology.

The successful applicant will have experience in developing ontologies for neuroscience, extensive knowledge/experience with the NIF Standard Ontology, and demonstrated project management skills.


● Develop ontologies based on key stakeholder requirements

● Map INCF ontologies to the NIF Standard Ontology

● Lead the team responsible for the integration of key neuroscience databases into KnowledgeSpace Area of responsibilities/duties

● Survey the INCF European community to determine their ontology requirements

● Develop ontologies that support the needs of the INCF European community

● Map INCF ontologies to the NIF standard ontology

● Integration of new resources into KnowledgeSpace



Masters in a Neuroscience related field.

3+ years experience working in experimental biology or neuroscience laboratories.

3+ years maintaining or developing ontologies.



MSc in Computer Science, Software Engineering, Electrical Engineering, Information Technology, and/or related technical discipline.

5+ years’ experience in a technical field.

SKILLS Required:

Python, knowledge of rdflib, general Linux/Unix experience with bash or other unix shell and associated utilities, and SQL. Ontology engineering using OWL2.

Knowledge of Protege, SPARQL, DL query, elk, Fact++, and Hermit.

Familiarity with the serialization formats commonly used in the bioontology world, turtle, rdfxml, obo, etc. Java with knowledge of OWLAPI and SciGraph.

A fast learner and a problem solver with an optimistic approach to challenges.

Proven ability to communicate effectively with technical and non-technical colleagues. Emphasis will be put on technical excellence, interpersonal skills, and initiative.


Experience with large data sets/analysis, Hadoop, scientific computing.

Training or experience with distributed programming environments such as Hadoop/ MapReduce.

Familiarity with neuroinformatics infrastructures.

Travel Statement

This position may require overnight travel up to 20% of the time and involve some irregular working hours due to collaboration in different time-zones.


The position is a 6-month contract.

Application process

Applications should include:

• A complete CV

• Contact information

• Contact details of at least 2 referees including at least one immediate supervisor

The application is to be submitted on the MyNetwork recruitment system.

Please send in your application as soon as possible, since we would like to meet candidates continuously during the application period.

Type of employment Temporary position 3-6 months
Contract type Full time
First day of employment as soon as possible
Salary monthly salary
City Solna
County Stockholms län
Country Sweden
Reference number 2-4554/2017
  • Louise Erixon, 0852487093
Union representative
  • Henry Wölling, SEKO, 08-524 840 80, henry.wolling@ki.se
  • Cecilia Björkdahl, SACO , 08-524 872 65
  • Anne Edgren, OFR/S, P, O, 08-616 16 29
Published 06.Oct.2017
Last application date 17.Oct.2017 11:59 PM CET

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