SIFRm
Semantic Indexing of French Biomedical Data Resources - mobility
Total Cost €
0EC-Contrib. €
0Partnership
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Project "SIFRm" data sheet
The following table provides information about the project.
| Coordinator |
UNIVERSITE DE MONTPELLIER
Organization address contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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, CleÌment; 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 MartÃnez-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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