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SIFRm

Semantic Indexing of French Biomedical Data Resources - mobility

Total Cost €

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EC-Contrib. €

0

Partnership

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 SIFRm project word cloud

Explore the words cloud of the SIFRm project. It provides you a very rough idea of what is the project "SIFRm" about.

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Project "SIFRm" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITE DE MONTPELLIER 

Organization address
address: 163 RUE AUGUSTE BROUSSONNET
city: MONTPELLIER
postcode: 34090
website: www.umontpellier.fr

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country France [FR]
 Project website http://www.lirmm.fr/sifr
 Total cost 264˙668 €
 EC max contribution 264˙668 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2015
 Funding Scheme MSCA-IF-GF
 Starting year 2016
 Duration (year-month-day) from 2016-09-01   to  2019-10-15

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITE DE MONTPELLIER FR (MONTPELLIER) coordinator 264˙668.00
2    BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY US (STANFORD) partner 0.00

Map

 Project objective

The Semantic Indexing of French Biomedical Data Resources (SIFR - www.lirmm.fr/sifr) project investigates the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of biomedical data. We will build and improve an ontology-based indexing workflow (Annotator) similar to what exists for English but specialized for other EU languages, starting with French. This will be the first step in offering semantic and multilingual search and mining of biomedical data resources. Our main goal is to enable straightforward use of ontologies freeing health researchers to deal with knowledge engineering or multilingualism issues and to concentrate on biological/medical challenges. SIFR (2013-2017) is a collaborative action between LIRMM & BMIR currently mainly funded by the French National Research Agency (ANR) Young Researcher program. This proposal (SIFRm) aims to fund the mobility of Dr. Clement Jonquet, SIFR’s principal investigator, assistant professor at LIRMM, to Stanford University. Stanford BMIR, head by Pr. Musen, is a worldwide leader providing (English-)ontology-based services to assist health professionals in the design of biomedical knowledge-based systems. BMIR is the birthplace of tools such as Protégé or BioPortal and scientific methodologies such as data driven medicine that Dr. Jonquet will acquire and reuse in a multilingual (e.g., French) and multidisciplinary (e.g., agronomy) context. During the return phase, a secondment is planned within INRIA ZENITH team, head by Dr. Valudriez, renown for distributed big data management. SIFRm will enable development of innovating scientific services to make annotation goes beyond English and reach another level in terms of variety and amount of data, e.g., French electronic health records. The project is a great career opportunity and guarantees a 2-way knowledge transfer between EU & US (informatics & biomedical skills).

 Publications

year authors and title journal last update
List of publications.
2019 Clement Jonquet
Semantic Indexing of French Biomedical Data Resources
published pages: 16-19, ISSN: 2632-4067, DOI:
Project Repository Journal 3 2020-02-12
2018 Anne Toulet; Biswanath Dutta; Clement Jonquet
Assessing the Practice of Ontology Metadata: A Survey Result
published pages: , ISSN: , DOI: 10.5281/zenodo.3484530
1 2020-02-12
2019 Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli, Adrien Coulet
PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-019-2693-9
BMC Bioinformatics 20/S4 2020-02-12
2019 Clement Jonquet
Ontology Repository and Ontology-Based Services – Challenges, contributions and applications to biomedicine & agronomy
published pages: , ISSN: , DOI:
University of Montpellier HDR manuscript 2020-02-12
2018 Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clement Jonquet
SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-018-2429-2
BMC Bioinformatics 19/1 2020-02-12
2017 Jonquet , Clement
Challenges for ontology repositories and applications to biomedicine & agronomy
published pages: , ISSN: , DOI:
SIMBig: Symposium on Information Management and Big Data 1 2020-02-12
2018 Fabienne Kettani, Stéphane Schneider, Sophie Aubin, Robert Bossy, Claire François, Clement Jonquet, Andon Tchechmedjiev, Anne Toulet, Claire Nédellec
Projet VisaTM : l\'interconnexion OpenMinTeD – AgroPortal – ISTEX, un exemple de service de Text et Data Mining pour les scientifiques français
published pages: 247-249, ISSN: , DOI:
29emes Journées Francophones d\'Ingénierie des Connaissances 2020-02-12
2017 Esther Dzale Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Hanna Ćwiek-Kupczyńska, Robert P. Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte, Pierre Larmande, Cyril Pommier, Vassilis Protonotarios, Carmen Reverte, Rosemary Shrestha, Imma Subirats, Aravind Venkatesan, Alex Whan, Hadi Quesneville
Developing data interoperability using standards: A wheat community use case
published pages: 1843, ISSN: 2046-1402, DOI: 10.12688/f1000research.12234.1
F1000Research 6 2020-02-12
2018 Clement Jonquet
Maitriser une technologie de gestion des ontologies et vocabulaires en France : défis et enjeux
published pages: , ISSN: , DOI:
SemWeb.Pro 2018 2020-02-12
2018 Clement Jonquet, Anne Toulet, Biswanath Dutta, Vincent Emonet
Harnessing the Power of Unified Metadata in an Ontology Repository: The Case of AgroPortal
published pages: 1-31, ISSN: 1861-2032, DOI: 10.1007/s13740-018-0091-5
Journal on Data Semantics 2020-02-12
2007 Abdaoui, Amine; Tchechmedjiev, Andon; Digan, William; Bringay, Sandra; Jonquet, Clement
French ConText: Détecter la négation, la temporalité et le sujet dans les textes cliniques Français
published pages: , ISSN: , DOI:
4ème Symposium sur l\'Ingénierie de l\'Information Médicale, SIIM\'17 2020-02-12
2017 Jonquet, Clement; Toulet, Anne; Emonet, Vincent
Two years later: the landscape of vocabularies and ontologies in the AgroPortal
published pages: , ISSN: , DOI:
5th International Workshop on sources and data integration in agriculture, food and environment using ontologies (IN-OVIVE @ EFITA 2017) 2020-02-12
2017 Jonquet, Clement
AgroPortal: an ontology repository for agronomy
published pages: , ISSN: , DOI:
European conference dedicated to the future use of ICT in the agri-food sector, bioresource and biomass sector, EFITA\'17, demonstration session 2020-02-12
2017 Tchechmedjiev, Andon; Jonquet, Clement
Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation
published pages: , ISSN: , DOI:
Language, Ontology, Terminology and Knowledge Structures Workshop (LOKTS 2017) 2020-02-12
2017 Monnin, Pierre; Jonquet, Clément; Legrand, Joël; Napoli, Amedeo; Coulet, Adrien
PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units
published pages: , ISSN: , DOI: 10.7287/PEERJ.PREPRINTS.3140V1
Methods, tools & platforms for Personalized Medicine in the Big Data Era (NETTAB 2017 Workshop) 1 2020-02-12
2018 Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Soumia Melzi, Jitendra Jonnagaddala, Clement Jonquet
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+
published pages: 1962-1965, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty009
Bioinformatics 34/11 2020-02-12
2016 Jonquet, Clement; Tapi-Nzali, Mike-Donald; Bringay, Sandra; TAPI NZALI, Mike Donald; Eholié, Solène
MuEVo, a breast cancer Consumer Health Vocabulary built out of web forums
published pages: 10, ISSN: , DOI:
A. Paschke; A. Burger; A. Splendiani; M.S. Marshall; P. Romano. SWAT4LS: Semantic Web Applications and Tools for Life Sciences, 2016, Amsterdam, Netherlands. 9th International Semantic Web Applications and Tools for Life Sciences, 2016 1 2020-02-12
2018 Amina Annane, Zohra Bellahsene, Faiçal Azouaou, Clement Jonquet
Building an effective and efficient background knowledge resource to enhance ontology matching
published pages: 51-68, ISSN: 1570-8268, DOI: 10.1016/j.websem.2018.04.001
Journal of Web Semantics 51 2020-02-12
2018 Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
AgroPortal: A vocabulary and ontology repository for agronomy
published pages: 126-143, ISSN: 0168-1699, DOI: 10.1016/j.compag.2017.10.012
Computers and Electronics in Agriculture 144 2020-02-12
2017 Marcos Martínez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos, Mark A. Musen
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation
published pages: Journal of Biome, ISSN: 2041-1480, DOI: 10.1186/s13326-017-0128-y
Journal of Biomedical Semantics 8/1 2020-02-12
2017 Algergawy, Alsayed; Karam, Naouel; Klan, Friederike; Jonquet, Clement
Proceedings of the 2nd International Workshop on Semantics for Biodiversity, S4BioDiv\'17
published pages: , ISSN: , DOI:
2nd International Workshop on Semantics for Biodiversity (S4BioDiv 2017) 2020-02-12
2017 Amina Annane, Zohra Bellahsene, Faiçal Azouaou, Clement Jonquet
YAM-BIO – Results for OAEI 2017
published pages: 5, ISSN: , DOI:
System paper Ontology Alignment Evaluation Initiative 2017 Campaign 2020-02-12
2017 Tchechmedjiev, Andon; Abdaoui, Amine; Emonet, Vincent; Jonquet, Clement
ICD-10 coding of death certificates with the NCBO and SIFR Annotators at CLEF eHealth 2017
published pages: , ISSN: , DOI:
Working Notes of CLEF eHealth Evaluation Lab 2020-02-12
2017 Dutta, Biswanath; Toulet, Anne; Emonet, Vincent; Jonquet, Clement
New Generation Metadata vocabulary for Ontology Description and Publication
published pages: 173-185, ISSN: , DOI:
11th Metadata and Semantics Research Conference, MTSR\'17 2020-02-12

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