Ontology-based indexing workflow (i.e., French Annotator) similar to what exists for English resources but dedicated and specialized for French
http://bioportal.lirmm.fr/annotator
This service is available within a portal of ~28 French biomedical ontologies/terminologies which reuse the BioPortal technology, developed at Stanford University. Ontologies has been offered by the CISMEF group from Rouen University Hospital, or taken from the UMLS, or directly uploaded by users. The SIFR BioPortal has been released in June 2015.
Need of automated annotation methods
http://bioportal.lirmm.fr/annotator
Researchers have called for the need of automated annotation methods and for leveraging natural language processing tools in the curation process. Still, even if the issue is being currently addressed for English, French is not in the same situation: there is little readily available technology (i.e., “off-the-shelf” technology) that allows the use of ontologies uniformly in various annotation and curation pipelines with minimal effort.
PARTNERS
Publications
66 scientific communications
All project communications are uploaded to HAL.
9 international journal, 2 national journal, 29 international conferences or workshops (such as ISWC, IDEAS, MIE, KEOD, MEDINFO).
Project Outcomes
SIFR Annotator
Design, development and deployment of the French Annotator
A publicly accessible ontology-based annotation tool to process French biomedical text data. A service that for a given piece of text will return biomedical ontology concepts directly mentioned in the text or semantically expanded.
See details in this publication: 10.1186/s12859-018-2429-2
OTHER RESEARCH
Obtain new research results to exploit and enhance ontology-based indexing services
- We achieved an exhaustive comparison of CISMeF HMTP and NCBO BioPortal, including the comparison of the annotation workflow and made CISMEF terminologies exportable.
- We work on multilingual mappings reconciliation and creation between French and English biomedical ontologies/terminologies.
- We work on automatic detection of emotion on public heath forums using text mining techniques. And we are building a patient vocabulary out of public patient-written resources.
- We work on improving biomedical ontology alignment using background knowledge.
- We work on formalizing consumer health vocabularies (cf. MuEVO)
DEVELOPMENT
24+ repositories on GitHub, 18 contributors
We actively reuse the technology of the US National Center for Biomedical Ontology and develop new features and software for our research.
SIFR BioPortal
An open platform to host French biomedical ontologies and terminologies based on the technology developed by the National Center for Biomedical Ontology
BioTex
Methodology and tool for automatic extraction of biomedical terms from plain text
Using existing extraction methods (e.g., C-Value) as well as keyword based indexing methods (e.g., Okapi, Tf-Idf) usually employed in information retrieval
NCBO Annotator+
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+
A web service which incorporates new functionalities within the NCBO Annotator
AgroPortal
A vocabulary and ontology repository for agronomy
We kicked-off the AgroPortal project and platform which goals is to offer a reference ontology repository for agronomic, plant sciences, nutrition and biodiversity
ViewpointS
A formalism for subjective knowledge
We work on semantic indexing and knowledge representation with the goal of capturing formal data and informal contributions into an evolutionary knowledge graph
Team
Over the 6 years of the project (2013-2019), the team included:
Clement Jonquet
Principal Investigator
Assistant Professor (LIRMM). Leader of the project. Selected as "Young Researcher" by French ANR and Marie Curie Fellow by H2020
Mathieu Roche
Co-PI (young researcher)
Researcher (CIRAD)
Sandra Bringay
Co-PI (young researcher)
Professor (LIRMM)
Vincent Emonet
Developer
(funded by ANR SIFR)
Juan Antonio Lossio Ventura
PhD student
(funded by Univ. of Montpellier)
Guillaume Surroca
PhD student
(funded by ANR SIFR)
Amina Annane
PhD student
Collaboration with ESI (Algiers)
Amine Abdaoui
Postdoc
(funded by ANR PractikPharma)
Andon Tchechmedjiev
Postdoc
(funded by ANR PractikPharma)
Dissemination
Events
Conferences, hackathons, meetup, tutorial, etc.
- 2 internal "scientific days" and 1 hackathon
- Web Science Montpellier Meetup
- AgroHackathons
- Tutorial: "SIFR BioPortal & AgroPortal : gestion d’ontologies et d’alignements pour les communautés biomédicales et agronomiques" organized in conjunction with IC 2016 in Montpellier. Slides of the tutoriel here.
- ESWC 2013 (~350 participants) and NLDB 2014 (~100 participants) in Montpellier
- SIMBig 2014 and 2015 conferences in Peru (thanks A. Lossio)
- French IC 2016 conference and IA & Santé workshop in Montpellier
Presentations
Multiple presentations uploaded on Slideshare, including
- Challenges for ontology repositories and applications to biomedicine & agronomy. C. Jonquet - Keynote at SIMBig’17 – Sept 6th 2017 – Lima, Peru.
- AgroPortal : a vocabulary and ontology repository for agronomy, plant sciences, biodiversity and nutrition. C. Jonquet - Latest presentation on AgroPortal. June 2017.
- SIFR BioPortal : Un portail ouvert et générique d’ontologies et de terminologies biomédicales françaises au service de l’annotation sémantique, C. Jonquet - DSSIS (réunion sur les serveurs mult terminologiques) - Paris, France, Juin 2017.
- A few contributions of the SIFR (Semantic Indexing of French biomedical Resources project) and how we reuse NCBO technology. C. Jonquet - Keynote at RISE'15 - June 30th 2015, Rennes, France.
- About the use of biomedical ontologies to play with text in the context of the SIFR project. C. Jonquet (with content also from J.A. Lossio) - Conférence invitée au LGI2P - Nimes, France - March 17th 2015.
- Kickoff meeting at ANR for JCJC projects 2013. C. Jonquet - Jan 24th 2013 - Paris, France.
Working group activities
- RDA Wheat Interoperability Working Group
- RDA Agrisemantics Working Group
- RDA Vocabulary and Semantic Services Working Group
- French GDR SemanDiv
- AgBioData Working Group
Talking about us ...
- AIMS Newsletter no.63, June 2017
- SIMBig Conference interview, September 2017
- INIST's Sequence de Com, December 2017
- Project Repository Journal, October 2019
- CORDIS web site, March 2020
- CNRS Hebdo, April 2020
Support & Funding
SIFR was mainly supported by ANR and H2020
JCJC program
This project has received funding from the French National Research Agency (ANR) under the Young Researcher program grant ANR-12-JS02-01001.
MSCA program
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 701771 (Marie Skłodowska-Curie Individual Fellowship).
Other sources of support included
Scientific council PhD program
PICS program
Visiting Student Researcher program
Eiffel fellowship
