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PhD position available in Montpellier, France (semantic web, biomedical ontologies, text mining)

From: Clement Jonquet <jonquet@lirmm.fr>
Date: Thu, 5 Jul 2012 16:25:01 +0200
To: "Clement Jonquet" <jonquet@lirmm.fr>
Message-ID: <05a201cd5aba$03496150$09dc23f0$@lirmm.fr>
The LIRMM (Informatics lab) is a 350-person cross-faculty research entity of
University of Montpellier, France and the National Center for Scientific
Research (CNRS). It is home of internationally recognized researchers in
semantic technologies, text/data mining, ontologies, bioinformatics and
artificial intelligence.


We are currently offering 1 fully-funded PhD studentships commencing fall
2012 for 3 years. Applications are invited from France, EU and international
students on the following PhD project.


All applicants must have a Master degree in Informatics or equivalent and
must demonstrate an excellent CV. Skills with semantic web and natural
language processing technologies are essential as well as good web
development capabilities. Some French speaking is preferred considering the
subject (but not mandatory).




Title: Using biomedical ontologies for semantic indexing of French
biomedical data resources


Institution:  <http://www.univ-montp2.fr> University of Montpellier,
<http://www.edi2s.univ-montp2.fr> I2S doctoral school


Where:  <http://www.lirmm.fr/> Laboratory of Informatics, Robotics, and
Microelectronics of Montpellier (LIRMM) 


Key-words: semantic web, annotation, (biomedical) ontologies, semantic
indexing, text/data mining, linked data, biomedical data


Context: The volume of data in biomedicine is constantly increasing. Despite
a large adoption of English in science, a significant quantity of these data
uses the French language. Usually, the content of the resources is indexed
to enable querying with keywords. However, there are obvious limits to
keyword-based indexing: use of synonyms, polysemy, lack of domain knowledge.
The community has turned toward ontologies to design semantic indexes of
data that leverage the medical knowledge for better information mining and
retrieval. However, besides the existence of various English tools, there
are considerably less ontologies available in French and there is a strong
lack of related tools and services to exploit them. This lack does not match
the huge amount of biomedical data produced in French, especially in the
clinical world (e.g., electronic health records). 

We will investigate the scientific and technical challenges in building
ontology-based services to leverage biomedical ontologies and terminologies
in indexing, mining and retrieval of French biomedical data. We will build
an ontology-based indexing workflow similar to what exists for English
resources (e.g., NCBO Annotator) but dedicated and specialized for French
and make it available as a service for the community. We will investigate
issues related to multilingual knowledge representation (complex alignments
between multilingual ontologies) and maintenance/evolution of created
annotations and mappings over time. Especially, the use of the
French-English mappings will enable us to index French resources using
English ontologies and to search English resources, already indexed with
English ontologies. We will also investigate the use of the indexing
workflow in the process of lifting data in the web of linked data. The
project will partially reuse the work done by the NCBO project, led by
Stanford BMIR. We will also capitalize upon existing tools developed by
CISMeF. Methods will be generalizable to other languages and domain of


Subject: The ontology-based workflow will use the semantics that the
ontologies encode (properties, hierarchies, mappings, semantic distance,
multilingualism and disambiguation) in order to improve the annotation
process. The PhD project will consist in participating to that workflow
working on French concept recognition (using NLP approaches),
disambiguation, multilingual alignments and ontology enrichment. Validation
will be achieved by processing use case derived biomedical data such as
electronic medical records, patient data publicly available on the Web, or




Supervisors: Dr. Clement Jonquet et Dr. Mathieu Roche


Collaborations: Catalogue et Index des Sites Médicaux de langue Française
(CISMeF) <http://www.cismef.org> , CHU de Rouen (Pr. Stefan Darmoni),
<http://bmir.stanford.edu/> Stanford Center for Biomedical Informatics
Research (BMIR), Stanford University (Pr. Mark Musen). Several visits are
planned with those groups.


When: Fall 2012 for 3 years


Application: For more information about this position, please contact Dr.
Clement Jonquet ( <mailto:jonquet@lirmm.fr> jonquet@lirmm.fr) and Dr.
Mathieu Roche ( <mailto:mroche@lirmm.fr> mroche@lirmm.fr). To apply, please
e-mail them the following:

-          an explanation of your interest in the proposed research field;

-          a curriculum vitae;

-          copies of diplomas and other relevant certificates;

-          a complete list of courses attended and corresponding grades;

-          names and contact details of referees.





Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor


 <mailto:jonquet@lirmm.fr> jonquet@lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 


                University of Montpellier


                161 rue Ada 
                34095 Montpellier Cdx 5



Tel:                +33/4 67 14 97 43     

Fax:               +33/4 67  41 85 00

Skype:          clementpro

Twitter:         <http://twitter.com/jonquet_lirmm> @jonquet_lirmm

Slideshare:   <http://www.slideshare.net/jonquet> jonquet




Received on Thursday, 5 July 2012 14:35:15 UTC

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