Research Jobs in Bioinformatics, University of Amsterdam
Netherlands. Three years postdoctoral positions within The Swammerdam Institute for Life Sciences (SILS). The successful applicants will work in a research project entitled “The development of a knowledge base framework for biomedical information“. Based on a full-time appointment (38 hours per week), the salary will range from €2330 to €3678 gross per month (salary scale 10) depending on the appointee’s expertise and experience.
The Institute is looking for an enthusiastic candidate with a background preferably in informatics/bioinformatics and knowledge of or a clear affinity with molecular biology, biochemistry and biomedical sciences.
The candidate should meet the following requirements:
- PhD in a relevant scientific discipline (e.g. informatics/bioinformatics)
- Experience with bioinformatics research
- Excellent software development skills (Java, Java frameworks (J2E, JENA, AJAX), web applications, relational databases)
- Extensive knowledge of OWL, RDF and XML
- Sufficient social skills to perform optimally in a dynamic scientific team and willingness to collaborate with colleagues from the AMC.
Project Description
An important area of life sciences research involves the elucidation of molecular mechanisms underlying complex disorders. One challenge is the acquisition, organization and integration of data and domain knowledge for specific biomedical domains or diseases. This project is a collaboration with the Academic Medical Centre (AMC, Amsterdam) and focuses on the development of a knowledge base for specific biomedical domains. You will be working in a larger team.
We have already constructed a first framework of the knowledge base system, and used it to implement a peroxisome knowledge base. Within this framework, information is presented by graphical concept maps (complemented with meta-data). However, the format underlying the concept maps is provided by OWL (Web Ontology Language).
In addition, we defined an initial OWL ontology (generic knowledge model) that represents the biomedical domain and on which we base the concept maps to ensure consistency and future application of the knowledge. One of the current challenges is to redefine and optimize the generic knowledge model such that it (a) correctly represents the heterogeneous biomedical domain, (b) becomes consistent, logical and extendible, (c) can be used for future applications (e.g. reasoning, integration with experimental data) and (d) can be integrated with existing biomedical vocabularies and ontologies.
Tasks
The main tasks of the postdoc will be to:
- Model the OWL generic knowledge model
- Integrate the OWL concept maps and generic knowledge model with existing vocabularies and ontologies
- Develop new applications of the knowledge base.
Further information can be obtained from:
Prof. A.H.C. van Kampen,
email a.h.vankampen@amc.uva.nl.
tel. +31 20-5667096/+31-20-5256547/+31-6-41768067
Applications (comprising a detailed curriculum vitae and a cover letter) should be emailed to application@science.uva.nl, quoting the job reference number (08-1007) in the subject line.
Applications may also be sent to:
Personnel Department
University of Amsterdam, Faculty of Science,
Kruislaan 404, 1098 SM Amsterdam, The Netherlands.
They too should comprise a detailed curriculum vitae and a cover letter. Please quote the job reference number (08-1007) and write ‘strictly confidential’ in the upper left-hand corner of the envelope.
All applications should be sent before 6 June 2008.
