Bonjour, Hello,
The LIRMM (University of Montpellier & CNRS) and CISMeF (LITIS, & Rouen School of Medicine) are currently offering 1 fully-funded PhD studentships commencing fall 2013 for 3 years.
Applications are invited from France, EU and international students on the following PhD project.
Sorry for multiple receptions. Thank you for transferring to your local students mailing lists.
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Title:
Semantic portals interoperability and multilingual data integration in biomedicine.
Information:
Institution: University of Montpellier, I2S doctoral school
University of Rouen, SPMII doctoral school
University of Rouen, SPMII doctoral school
Supervisors: Clement Jonquet (LIRMM, UM2) – jonquet@lirmm.fr
Lina Soualmia (LITIS, CHU de Rouen) – lina.soualmia@chu-rouen.fr
Stefan J. Darmoni (LITIS, CHU de Rouen) – stefan.darmoni@chu-rouen.fr
Lina Soualmia (LITIS, CHU de Rouen) – lina.soualmia@chu-rouen.fr
Stefan J. Darmoni (LITIS, CHU de Rouen) – stefan.darmoni@chu-rouen.fr
Project: SIFR project (Semantic Indexing of French Biomedical Data Resources)
When: Fall 2013 for 3 years
Where: Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM)
(2 first years)
Catalogue et Index des Sites Médicaux de langue Française (CISMeF)
(last year)
(2 first years)
Catalogue et Index des Sites Médicaux de langue Française (CISMeF)
(last year)
Collaborations: Stanford Center for Biomedical Informatics Research (BMIR),
Stanford University (Pr. Mark Musen).
Stanford University (Pr. Mark Musen).
Key-words:
(biomedical)ontologies & terminologies, semantic web, multilingualism, knowledge representation, biomedical data integration, semantic interoperability, ontology alignment, linked 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. The community has turned toward terminologies and 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).
Within the SIFR project, 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 use this workflow for semantic indexing of French biomedical data. 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 multilingual (French-English) mappings will enable us to index French resources using English ontologies and to search English resources, already indexed with English ontologies. We envision potential interesting result in semantic search and automatic translation. We will also investigate the process of lifting the annotated 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 domains of application.
Subject:
The community has already invested efforts in developing ontology Web portals to assist health professionals and users in the use of biomedical ontologies and terminologies (e.g., browsing, visualizing, commenting and indexing). For instances, BioPortal (http://bioportal.bioontology.org) & HeTOP (http://www.hetop.eu) developed respectively by Stanford University and CISMeF.
The PhD project will consist in investigating the technological and scientific issues to enable semantic interoperability of BioPortal and HeTOP but also ontology portals in general. Also, the project will use semantic web methodologies and technologies to extract and represent multilingual mappings (i.e., alignments) between biomedical ontologies and use these mappings to enable multilingual indexing and search of biomedical data. Possible application to automated translation could be also considered.
Detailed Description:
http://www.lirmm.fr/sifr/positions/2013_SIFR_PhD_position.htmlApplication:
For more information about this position, please contact Clement Jonquet (jonquet@lirmm.fr), Lina Soualmia (lina.soualmia@chu-rouen.fr) and Stefan J. Darmoni (stefan.darmoni@chu-rouen.fr). To apply, please e-mail 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.
Master students in informatics/computer science. Experience in semantic web technologies and good software/web engineering capabilities are highly preferable.- 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.
Motivation for the subject is mandatory and personal initiatives is a must have. You will be at the center of a 3-part collaboration with LIRMM-CISMeF-NCBO.
We strongly recommend a perfect knowledge of English and a good knowledge of French.
Best regards,
CJ
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Dr. Clement JONQUET - PhD in Informatics - Assistant Professor
PI of the SIFR project: Semantic Indexing of French Biomedical Data Resources (ANR, UM2, CNRS)
University of Montpellier Tel: +33/4 67 14 97 43
LIRMM Fax: +33/4 67 41 85 00
161 rue Ada Skype: clementpro
34095 Montpellier Cdx 5 Twitter: @jonquet_lirmm
34095 Montpellier Cdx 5 Twitter: @jonquet_lirmm
France Google: jonquet.lirmm@gmail.com
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