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EBI Job vacancy: Ontologist

Evelyn Camon camon at
Wed Sep 7 02:41:11 PDT 2005


I am forwarding this job advertisement to GO friends on behalf of 
Susanna Sansone (EBI)
Toxicogenomics Project Coordinator with the Microarray group 
(sansone at


Visit EMBL Job advert at:

EMBL site: Hinxton, near Cambridge, UK

Commencing date: As soon as possible after closing date

Job description: Data standards and object models are being developed 
for a variety of functional genomics domains. Many of these object 
models include a reference to an ontology concept in order to provide a 
rich set of terms for annotation. Incorporation of ontologies in the 
experimental annotations will provide semantics for these biological 
features relevant to the interpretation and comparison of functional 
genomics investigations.
We are looking for an ontologist to participate in the development of a 
Functional Genomics Ontology (FuGO), a large international collaborative 
effort that builds on the MGED Ontology (MO) providing terms to be used 
for the microarray workflow. The post holder will gather, analyze and 
accurately categorize biological knowledge from diverse functional 
genomics investigations, contributing to the development of ontological 
structures to satisfy the general requirement of facilitating the 
high-level description of an investigation. In particular the post 
holder will lead the creation of ontological structures for metabolomics 
applications, as part of a BBSRC e-Science Programme grant. According to 
the post holders skills and interests, the project offers the 
opportunity to explore knowledge elicitation methodologies, the use of 
text mining technologies and groupware tools for maintain the ontology. 
The project is an exciting opportunity for the post holder to work 
closely with the groups from the MGED Society, HUPO-PSI and Metabolomics 
Society, as well as ontology engineering experts of the Ontogenesis Network.

Qualifications and experience: A PhD and a background in Computational 
Linguistics or Computer Science are required. An additional biological 
or bioinformatics qualification is desirable. The ideal candidate will 
have experience in developing and maintaining ontology structures in a 
team setting. OWL language and Protege tool are required, and some 
knowledge of XML, Perl and/or Java would be advantageous. The position 
also requires familiarity with web-related technologies as well as UML 
and object oriented design principles. Excellent oral and written 
communication skills are required, as the post holder is required to 
communicate effectively with users and collaborators as well as 
eliciting and accurately presenting information. Not only must the 
person be able to work on a project from start to finish independently 
as well as being a part of a team, but also (s)he must be able to 
readjust priorities to meet deadlines.

Contract: An initial 2 year contract will be offered to the successful 
candidate, with a possibility of extension depending on the availability 
of funding.

Closing date: 16 October 2005

Web page:

EMBL is an inclusive, equal opportunity employer offering attractive 
conditions and benefits appropriate to an international research 

Please note that EMBL does not return CVs or attached documents to 

For further information please contact Dr. Susanna-Assunta Sansone at: 
sansone at

To apply for this position, please email a detailed CV with concise 
description of research experience and the names and addresses of at 
least two referees, quoting W/05/PD/20 in the subject line to: 
application at

Personnel, EMBL, Postfach 10.2209, 69012 Heidelberg, Germany.

Fax: +49 6221 387555 E-mail: application at

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