PhD
in Informatics
Senior Researcher, INRAE &
Associate Researcher, University of Montpellier
ORCID: 0000-0002-2404-1582
Born May 26, 1980, Nîmes (Gard), France,
married, 2 children, French nationality.
|
INRAE – MISTEA |
TEL: (+33/0) 467 41 97 43 |
§
§
Email:
jonquet@lirmm.fr – clement.jonquet@inrae.fr
§
Twitter: @jonquet_lirmm
§ Home
page: https://jonquet.mystrikingly.com
§
Public
profiles: Google Scholar, ResearchGate, DBLP, HAL, PubMed, CiteSeer.
§ Multidisciplinary research activities: ontologies, semantic Web, ontology repositories, biomedical informatics, semantic annotation, data integration,
metadata, knowledge graphs, text mining, service-oriented computing, Web
science, multi-agent systems.
§ Experience in applied research
(biomedicine, agronomy), software engineering & transfer skills.
§ (Co)author of 165 publications or communications
cumulating more than 4200 citations,
including 29 international journals in multiple domains, 6 as first author,
6 as last, and 84 conf/workshop articles.
§ Collaborative work experience, project funded research (EU, ANR, NIH),
management skills (project coordination, work-package leading, outsourcing,
supervision).
§ Principal investigator of 2 ANR projects
(one JCJC “young researcher”), Co-PI of 2 ANR projects, recipient of H2020 Marie Sklodowska-Curie grant. WP
lead of 1 Horizon Europe / EOSC project.
§ 9 years of various academic
teaching (~1400h
~TD) in Informatics/CS to different grades.
§ (Co)supervision of 27+ MSc. Students
& 5 PhD candidates, 9 postdocs/researchers, 7 engineers.
§ Mobility: 3-year postdoc and later
3-year visiting scholar at Stanford University.
Contact & Professional Situation
Scientific Influence and dissemination
Collaborations & Working groups
Detailed Seminars & Invited presentations
Summary of Teaching Activities
Focus on HDR (habilitation) synthesis (2019)
Postdoctoral Research Activity (2007-2010)
PhD Thesis Research Activity (2003-2006)
MSc Research Activity (2003 and before)
(French) Details des activités d’enseignement
Formation à la pédagogies suivies
Interventions diverses & Encadrements
§ Starting Sept. 2022: Senior Researcher (DR2), INRAE,
France.
Mathematics, Informatics
and STatistics for Environment and Agronomy (MISTEA).
§
Mathematics, Informatics and STatistics for Environment and Agronomy (MISTEA).
§
Researcher in the Laboratory of Informatics, Robotics, and Microelectronics of
Montpellier (LIRMM).
§ 2015-2018: Visiting scholar, Stanford University, USA.
Center for Biomedical Informatics Research (BMIR). Working with Pr. M. A. Musen & the NCBO.
§
Researcher in the Laboratory of Informatics, Robotics, and Microelectronics of
Montpellier (LIRMM) and teacher at Polytech Montpellier Engineering School.
§
Center for Biomedical Informatics Research (BMIR). Working within Pr. M. A. Musen's group.
§ 2006-2007:
Lecturer, University Montpellier 3,
France (humanities and social sciences) (~ French ATER). Researcher at LIRMM.
§ 2003-2006: French government PhD grant &
young lecturer at University Montpellier 2 (sciences and techniques) (~
French ‘allocataire MENRT’ & ‘moniteur CIES’).
§ 2019: HDR in Informatics – University of Montpellier (French research direction
habilitation)
§ 2006: PhD in Informatics/Computer Science (First class with distinction)
– Univ. Montpellier 2 (UM2)
§
§ 2001: BSc in Computer Science (2.2
honours) – UM2 (~ French Licence & DEUG)
§ 1998: High School Diploma
specialized in Maths (2.2 honours) – Uzès (Gard) (~ French Bac. S)
Current
Research Activity
I am
working in the semantic Web area, designing,
implementing, experimenting and evaluating scientific methods and technologies
for ontologies and their use. I am interested in knowledge engineering and
data interoperability issues, especially in the use of ontologies (or more
largely any semantic resources or artefacts) for knowledge representation,
extraction and sharing. I am an expert on ontology
repositories and ontology-based services (topic of my HDR) and I develop and maintain a scientific and
technical expertise on this subject especially through a partnership with
Stanford BMIR and the
development of the OntoPortal technology with the vision to promote data interoperability
and FAIR ontologies. This fairly applicative context allows me to investigate
scientific issues in several sub-fields of knowledge
engineering: semantic annotation, terminology extraction, linked-open data,
text mining, ontology alignment, metadata languages, knowledge graphs. I have
experience in the biomedical domain (NCBO & SIFR projects) –for instance on semantic
annotation and indexing of biomedical text or clinical notes– and my challenge
is to abstract and generalize informatics methods to other languages (e.g.,
French) and domains (e.g., agronomy, biodiversity). Today, I lead the D2KAB project, a 12-partner and 35-person ANR
research action
which focus on implementing methods to transform data into knowledge for
agronomy and biodiversity and in which we design a vocabulary and ontology
repository for agronomy and related domains (AgroPortal project). I am also involved in semantics related activities for the
development of the European Open Science Cloud (EOSC), especially as WP-lead in
the Horizon Europe FAIR-IMPACT project.
Research
Projects
§
§ 2022-2023: Member, VitisExplorer
(Information System to explore the agronomic and oenological potential of vine
genotypes) – PNDV – 3-partner project including INRAE (Colmar &
Montpellier) and IFV, head by E. Duchêne, INRAE.
§ 2022-2024: Member, DACE-DL (DAta-CEntric AI-driven Data
Linking) – ANR, 3-partner project including LIRMM & MISTEA, head by K.
Todorov, LIRMM.
§ 2020-2023: Principal Investigator
OntoPortal Alliance French pillar Labex NUMEX Int. Research Team, 3
partners.
§
§ 2019-2024: Principal investigator of D2KAB project (Data to Knowledge in Agronomy and Biodiversity) – ANR, 12-partner, 35-person project on
semantics and linked data in ag & biodiv.
§ 2017-2019: Co-principal investigator VisaTM project. Text & Data mining infrastructure
for French scientists. BSN-10 head by C. Nédellec, INRAE.
§
§
§ 2013-2019: Principal investigator of the Semantic Indexing of
French Biomedical Data Resources (SIFR) project – ANR Young
Researcher &
H2020 Marie Skłodowska-Curie Action. Building ontology-based services to leverage biomedical ontologies and
terminologies in indexing, mining and retrieval of French biomedical data. Also
supported by Univ. of Montpellier & CNRS, France-Stanford and Eiffel
programs.
§ 2012-2018: Member, Institut de
Biologie Computationnelle (IBC), axe 5 (workflow & data integration) –
ANR Inv. d’Avenir BioInfo. Development and use cases for AgroPortal &
AgroLD, head by E. Rivals.
§ 2011-2013:
Member, CR2i DiagnosTIC-Santé project (Centre
de Recherche et d'Innovation Industrielle) – Inv. d’Avenir PFMI. Member of the metadata repository
group (multi-omics platform development).
§
§ 2003-2007: Member, European Learning
Grid Infrastructure (ELeGI) – IST IP EU (FP6).
§ 2003-2004: Member, Learning Grid of
Excellence Working Group (LeGE-WG) – IST STREP EU (FP5).
Teams
& Research Groups
§ Since Sept. 2020: Member and coordinator
of the Informatics axe, MISTEA.
§ Since Sept. 2020: Associated member
of LIRMM WEB-CUBE team (Web Architecture, Semantic Web, Web of Data),
head by A. Castelltort and Pr. A. Laurent.
§ 2018-2020: Member, and co-head
with Pr. A. Laurent of LIRMM FADO team (Fuzziness,
Alignments, Data & Ontologies).
§ 2018-2020: Associated member (INRIA
delegation) of INRIA Sophia-Antipolis’s WIMMICS
team headed by F. Gandon
(social & formal semantics on the Web, linked data).
§ 2015-2018: Member of Pr. Musen’s lab
and until 2017 of Pr. M. Dumontier’s lab at Stanford BMIR (medical informatics, knowledge
representation and semantic Web (Protégé & BioPortal)).
§ 2010-2018: Member of the LIRMM SMILE team (multi-agent systems, Web science,
service-oriented computing, ontologies, serious games, simulation), head
by F. Michel.
§ 2007-2010: Member of Pr. M. Musen’s lab
and the NCBO team at Stanford BMIR (medical informatics, knowledge representation
and semantic Web (Protégé & BioPortal)).
§ March 2006: Associated member
(internship) of the UK’s Open University’s KMI group.
§ 2003-2007:
Member of the LIRMM’s KAYOU team (multi-agent systems, constraints, Web, Grid,
service-oriented computing, ontologies, collaborative learning).
Research
Topics
Ontologies
& vocabularies, Ontology repositories, Ontology-based services, Semantic
Web, Semantic annotation, Knowledge graphs, Biomedical Informatics, Ontology
alignment, FAIR data & metadata, FAIRness assessment, Linked Open Data, Knowledge
representation, Data integration, Information Retrieval, Text mining, Service-oriented
computing, Web Science, Distributed systems, Multi-Agents Systems, Applications
to biomedicine/health and agronomy/biodiversity.
Grants
(funding obtained as (co-)leader)
|
Project (#) |
Program |
Date |
Amount (Total) |
Type of support |
Collaboration |
Topic |
|
TUBO |
CNRS
PICS |
2011-2013 |
18K€ |
operating
costs |
Stanford
BMIR, CHU Rouen |
Ontology
repository interoperability |
|
French GDR STIC-Santé
collaborative actions |
2012 |
1K€ |
operating
costs |
CHU Rouen |
|
|
|
Univ. Montpellier 2 scientific council PhD student grant |
2012-2015 |
90K€ |
PhD
fellowship |
UMR
TETIS |
Terminology
extraction and ontology enrichment |
|
|
SIFR (ANR-12-JS02-0010) |
ANR JCJC
call 2012 |
2013-2017 |
277K€ |
project |
Stanford BMIR, CHU Rouen, UMR TETIS |
Semantic
indexing, ontology repositories, knowledge representation |
|
French CNRS, support for H2020 project preparation |
2014 |
3K€ |
operating
costs |
CIRAD |
Application
for EU project related to ViewpointS |
|
|
ANR IBC young researcher
grant (ANR-11-BINF-0002) |
2014 |
10K€ |
operating
costs |
|
Complement
for SIFR. Kick off of AgroPortal |
|
|
AgroPortal (ANR-10-LABX-20) |
Labex
NUMEV call |
2014-2015 |
46K€ |
1-year
engineer |
Multiple |
Building
first AgroPortal prototype |
|
PractiKPharma (ANR-15-CE23-0028) |
ANR generic
call 2015 |
2015-2019 |
137K€
(677K€) |
project |
LORIA (Nancy), HEGP (Paris), CHU St Etienne |
Electronic
health records text mining and pharmacogenomics |
|
SIFR mobility (GA 701771) |
H2020-MSCA-IF-2015 |
2016-2019 |
265K€ |
project |
Stanford
BMIR, INRIA (Wimmics) |
Support
for mobility in the context of SIFR & AgroPortal |
|
e-Tera (partner
of H2020 eRosa) |
ANR MRSEI |
2016-2017 |
5K€ (24K€) |
operating
costs |
INRA-DIST,
IRD |
Roadmap
for e-infrastructure in agri-food |
|
AgroPortal (ANR-11-BINF-0002) |
IBC
of Mont-pellier WP5 |
2016-2018 |
100K€ |
postdoc |
Multiple |
Community
support and outreach for AgroPortal |
|
VisaTM / AgroPortal |
BSN-10 |
2017-2018 |
15K€
(160K€) |
postdoc |
INRA-MaIAGE, CNRS-INIST |
Text
& data mining, semantic resources, infras |
|
Lingua / AgroPortal (ANR-10-LABX-0001-01) |
NUMEV-Agro-CEMEB
Interlabex |
2017 |
90K€ |
postdoc |
INRA
Montpellier, CNRS-CEFE |
Ontology
mapping lifecycle in AgroPortal. Collaboration with GACS |
|
EUDAT Semantic Working
group |
2018 |
6K€ (30K€) |
postdoc |
H2020
EUDAT, eScience Factory |
Ontology
portal interoperability |
|
|
H2020 OpenMinTed (OMTD) call for tender |
2018 |
15K€ |
postdoc |
H2020
OpenMinTed |
Text
& data mining, semantic resources |
|
|
D2KAB (ANR-18-CE23-0017) |
ANR generic
call 2018 |
2019-2023 |
(300K€)
950K€ |
project |
INRIA
(Wim-mics), INRA, IRSTEA, CEFE, ACTA |
Data
to knowledge in agronomy and bio-diversity. AgroPortal, and linked data |
|
Joint Montpellier-Stanford Laboratory |
CNRS
Int. Research Laboratory |
2019-2023 |
~14K€
(NA) |
operating
cost |
LIRMM,
Stanford (3 teams) |
Medical
robotics, underwater robotics and Semantic Web |
|
#DigitAg
internship and visiting scholar fellowships |
2020-2023 |
37K€ |
intern,
visit |
LIRMM,
INRAE, EP Thiès |
Agri-food
semantic resources, semantic annotation |
|
|
FooSIN (ANR-19-DATA-0019) |
ANR
flash open science 2019 call |
2020-2022 |
17K€
(80K€) |
project |
LIRMM,
INRAE, IRD (+CIRAD) |
French
participation to GO FAIR Food Systems Implementation Network |
|
OntoPortal
Alliance (ANR-10-LABX-20) |
NUMEV
Int. Research Team |
2020-2023 |
80K€ |
project |
LIRMM,
Stanford, LifeWatch, INRAE |
Ontology
repositories for biomedicine, agronomy and ecology |
|
DACE-DL (ANR-21-CE23-0019) |
ANR generic call 2021 |
2022-2024 |
128 K€ (410K€) |
project |
LIRMM, MISTEA,
IRIT |
Data
linking, semantic Web, machine learning |
|
VitisExplorer |
PNDV Appel Santé Vignoble 2021 |
2022-2023 |
77K€ (223K€) |
project |
INRAE Colmar, MISTEA, IFV |
Data
integration, data analysis, information system |
|
FAIR-IMPACT (GA 101057344) |
HORIZON-INFRA-2021-EOSC-01-05 |
2022-2024 |
665K€
(9,8M€) |
project |
DANS,
CSC, DCC, DeiC, Trust-IT |
EOSC
roadmap, FAIR digital objects, FAIR semantic artefacts |
|
#DigitAg PhD fellowships |
2023-2026 |
60K€
(120K€) |
PhD fellowship |
UMR
AIDA & TETIS (Cirad) |
Agroecology
scientific variables |
|
§
§ Doctoral research: Situated at the crossing of three
important domains: service-oriented computing (web service, components,
business process, etc.), multi-agent systems (modeling, interaction,
architecture) and Grid (resources sharing, Grid service, Grid computing). I
proposed in my thesis a new vision for the concept of “service”, called dynamic
service generation. This vision, based on interactions between agents
(human or artificial) and relying on a Grid infrastructure, enabled dynamic
construction of services based on the conversation between user & provider.
Two important contributions were: (i) STROBE: an agent communication and
representation model based on conversation contexts to enable interactive
specification of agent capabilities; (ii) Agent-Grid Integration Language
(AGIL): a grid-multiagent integrated model formalized with a description
language which leverages the stateful and dynamic aspect of Grid services.
§ ELeGI project research: I worked on a collaborative environment constructed over a Grid
infrastructure based shared desktops. We experiment the environment with a
community of chemists tackling the problem of collaborative construction of an ontology.
Ontologies,
Software Development & Technology
§ Design and part of the development
of the following semantic resources:
o
Metadata
for Ontology Description and Publication Ontology (MOD)
o
Brazilian
Thesaurus Agrícola Nacional (THESAGRO)
o
BBCH-based Plant Phenological
Description (PPDO)
o
Crop
Planning and Production Process Ontology (C3PO)
o
E-Phy
Ontology (E-PHY)
§ Since 2013, all development projects
are maintained on GitHub, as well as the issue trackers for scientific
traceability, reproducibility and openness:
o
https://github.com/sifrproject
o
https://github.com/agroportal
o
https://github.com/practikpharma
o
https://github.com/ontoportal-lirmm
o
https://github.com/FAIR-IMPACT
§
o
Key
contributor to the OntoPortal open-source project.
o
Technical
conception, design, vision and evaluation of the OntoPortal technology (“lirmm-branch” adopted by 5 partners of the OntoPortal Alliance).
o
Design
of O’FAIRe, an Ontology FAIRness Evaluator methodology for semantic resources,
implemented in AgroPortal and other OntoPortal installations.
o
Design
of French FastContext an adaptation of the ConText text
mining component for French.
o
o
Design,
development & maintenance of the SIFR/French Annotator and the NCBO
Annotator+ both included within the SIFR BioPortal.
o
Design
of YAM-BIO a tool for ontology alignment with background knowledge resources
(A. Annane’s PhD project).
o
Design
of Viewpoints, a graph-based system for collaborative knowledge representation
and learning (G. Surroca’s PhD project).
o
Design
of BioTex a tool for automatic extraction of biomedical
terms from text (J. Lossio’s PhD project).
o
Design
& development (in collaboration with LGI2P) of a semantic distance Web
service.
§
§ NCBO Annotator, Resource Index & Recommender (BioPortal URL + /annotator, /resources, /recommender). I was the main researcher (along with N. Shah,
PhD, MD) and architect of these 3 services (prototyping, testing, evaluation,
QA and deployment). I supervised 3 part time software developers working on
these projects during 2 years.
§ STROBE model, prototype
implementation of the multi-agent model designed during my PhD project.
§ Experimentation with the Grid
Shared Desktop developed
within the EleGI project.
Seminars
& Invited presentations
§ Over the last 14 years, I have been
invited for 5 keynotes at conference,
15 invited talks, 26 project or lab seminars, 15 team or group seminars, and a
few miscellaneous talks as described after.
§
§ I have 26 presentations on SlideShare cumulating ~15000 views.
Awards
& Distinctions
§ Best paper award at the 32èmes Journées Francophones d’Ingénierie des Connaissances (IC 21), July 2021.
§ 2nd best poster award at
the 14th Research Data Alliance plenary meeting (RDA P14), Oct. 2019.
§
§ Recipient of the EU Marie Sklodowska-Curie Action (GF-IF)
program (2016-2019). The MSCA program is very selective with a success rate
of around less than 10% on Individual Fellowships (GF).
§ 1st Prize at the 2nd
BD2K & 4th Network of BioThings Hackathon, Stanford, Nov. 2015.
§ French ministry distinction, Prime d'Excellence Scientifique (PES) 2013-2015 (stopped with mobility).
§ Recipient of the French National
Research Agency (ANR) Young Researcher
program, 2012. The program (JCJC) is very selective with less than 17%
success rate in 2013.
§ Honorable mention award at 3rd ACM Int. Conference on Web
Science (WebSci 2011), June 2011.
§ Selected in Pr. Russ Altman’s 2011 Year in Review for journal article about biomedical ontology
recommendation. AMIA Translational
Bioinformatics Summit (AMIA-TBI 2011), March 2011.
§
At
MISTEA
In
the informatics axe on ontology and knowledge engineering (C. Roussey), data
linking and knowledge graphs (D. Symeonidou), semantics and ontologies related
to grapevine (A. Charleroy & IFV), ontology-based software engineering and
use of ontologies with OpenSILEX (A. Tireau, A Charleroy) and many other matters
related to knowledge engineering (P. Neveu).
At
LIRMM
A part
from the contributions and exchanges related to the multi-agent systems & interaction
research group “SMILE” (S. Cerri), I have strongly interacted and worked with members
of other teams, especially the data and text mining “ADVANSE” team (S. Bringay,
M. Roche, M. Teisseire); the ontology alignment & linked data “FADO” team then
“WEB3” (Z. Bellahsene, K. Todorov, F. Scharffe); the big data and scientific workflow
“ZENITH” INRIA team (P. Valduriez, P. Larmande).
Within
the Montpellier research ecosystem
During
SIFR, I co-supervised 2 PhD students with researchers from UMR TETIS (M. Roche,
M. Teisseire, P. Lemoisson) between 2011 and 2015. The AgroPortal initiative rapidly
found an echo locally that have encouraged us to concretize the project in Montpellier.
Since 2014, it brought me to collaborate with UMR DIADE IRD (P. Larmande) on agronomic
linked data (AgroLD project) and AgroPortal; CIRAD (M. Ruiz), Bioversity International
(E. Arnaud), INRAE (P. Neveu, P. Buche), CNRS-CEFE (E. Garnier) on several use cases
for AgroPortal. More recently, I have started a partnership and exchanges with
ANR Convergence Institute #DigitAg (led
by V. Bellon-Maurel) for data interoperability projects on digital
agriculture. With #DigitAg and HE InterCropValues project, I co-supervise
another PhD with CIRAD (UMR TETIS (M. Roche) and AIDA (S. Auzoux)).
National
Collaboration
The
collaborations mainly happened during formal projects. Within SIFR, I started the
project with the CISMeF group of CHU Rouen (S. Darmoni), and then had multiple interactions
with other medical informatics organizations such as INSERM LIMICS (J. Charlet),
related to French biomedical ontologies, CHU Nancy (N. Girerd) on knowledge extraction
form electronic health records. Within the ANR PractiKPharma consortium, led by
LORIA (A. Coulet), I also collaborate with HEGP hospital (B. Rance & A. Burgun)
and CHU St Etienne (C. Bousquet). AgroPortal found interests with other INRAE research
groups (C. Pichot, C. Nédellec, C. Pommier) but also with INRAE’s DipSO (S. Aubin,
O. Hologne, E. Dzalé) with who I closely collaborate since 2016 on agri-food data
interoperability within AgroPortal, VisaTM, eRosa/eTera projects and several working
groups of the Research Data Alliance. Since 2017, both within VisaTM and the GDR
SemanDiv, I exchange with CNRS-INIST (C. Francois, D. Vachez) on accessing and sharing
semantic resources.
§ Since 2022: DataTerra
research infrastructure (G. Alviset, C. Pierkot, F. Huynh) and HE FAIR-EASE
project (A. Rizzo).
§ Since 2021: National partners of the OntoPortal Alliance: Ecole Nat. de Tarbes (M-H. Karray), and since 2022, Observatoire de
Paris (B. Cecconi).
§ Since 2021:
Partners from DACE-DL consortium: IRIT (C. Trojhan, O. Teste) and LIRMM (K.
Todorov).
§ Since 2019: Partners
from D2KAB consortium: ACTA (F. Brun), ex-IRSTEA (C. Roussey), CNRS I3S &
INRIA-Wimmics (C. Faron-Zucker, F. Michel, O. Corby).
§ Since 2017:
CNRS InEE GDR SemanDiv (E. Garnier) which focus on semantic
issues for biodiversity.
§ Current or past industrial exchanges include: Sanofi (T. Pages), Ontologos
(C. Million), Logixys/Algo.solutions (P. Dugénie), Mondeca
(F. Amardeilh), eScience Data Factory (Y. Le Franc), API-AGRO (T-P.
Haezebrouck), Elzeard (F. Amardeilh).
§ 2003-2006:
In the context of French STIC Santé working group or as a member of the French MFI working group (Formal Model of Interaction).
International Collaboration & Working
Groups
The context of AgroPortal projects
and application to agriculture brought me to join and work with several key
actors for data sharing and semantics in agri-food and biodiversity. Often
within international working groups (e.g.,
of the Research Data Alliance), such
as:
§
Since 2023: Embrapa, Brazil (M. Ambrosio Telles) and
the GTermos group.
§
Since 2020: International partners of the OntoPortal Alliance: LifeWatch ERIC (N. Fiore), CNR (I.
Rosati), Fraunhofer Materials (A.-A Todor), NFDI4Biodiversity (N. Karam)
§ Since 2023: Horizon
Europe EOSC project Technology Group and Opportunity Areas 2 (Metadata, Ontologies & Interoperability)
gathering members of projects funded in the INFRA-EOSC program.
§ Since 2022: Horizon Europe FAIR-IMPACT project partners and others in the context
of EOSC.
§
Since 2017: RDA Vocabulary and Semantic Services
Interest Group. Co-leader of
the ‘ontology metadata’ task group, then member of the I-ADOPT working group.
Other ongoing collaborations:
§
2018-2019: With multiple European consortia to prepare unsuccessful responses to H2020 following calls:
DT-ICT-08-2019, INFRAEOSC-02-2019, DT-SFS-26-2019 and MSCA-ITN-2019&2020.
§
Since 2016: Indian Statistical Institute (B. Dutta), on ontology metadata.
§
Since 2011: Stanford BMIR (M. Musen), with the Protégé & NCBO groups. This long-lasting collaboration supported by different programs allowed
me to develop an expertise in Montpellier on ontology services and repositories.
Past collaborations:
§
§
2019-2021: GO FAIR Food Systems Implementation Network.
§
2017-2019: H2020 eRosa project (e-infrastructure Roadmap for Open Science in Agriculture)
community and especially with INRAE, Wageningen UR, AgroKnow and Food
Agriculture Organization.
§
2018:
H2020 OpenMinTeD (text mining platform) H2020 project in the context of 2nd
call for tender.
§
2016-2018: GACS working group (J. Keyser, I. Subirats), design of the Global
Agricultural Concept Scheme based on FAO’s Agrovoc, USDA Nat. Agriculture
Library, and CAB Int. thesauri.
§
2016-2018: AgBioData which gathers model organism databases in agriculture (mostly in the
US).
§
2016-2008: Godan (Global Open Data for Agriculture and Nutrition) Action project
and FAO (V. Pesce) on the Agrisemantics Map of Data Standards.
§
§
2016-2017: RDA Wheat Data Interoperability working group (E. Dzalé), as a use
case for AgroPortal.2015-2016: Stanford
BMIR (M. Dumontier) as a member of the research group.
§
2016: Univ. of Sao Paulo and Univ. Fed.
de Tocantins (D. Prata) for a joint CAPES-COFECUB project on spatial and
temporal data about biodiversity in Amazonians conservation.
§
2007-2010: NCBO collaborators and community: Univ. of Colorado School of Medicine (L. Hunter),
Univ. of California San Francisco (I. Sim), Medical College of Wisconsin
(S. Twigger), Wright State Univ. (A. Sheth), Goal: leverage NCBO
solutions within biomedical sciences scenarios.
§
2004-2006:
A. Krief’s lab, Notre Dame de la Paix Univ., Namur, Belgium. Collaborative construction of ontology for chemistry.
§
2003-2006: Knowledge Media Institute (KMI), Open Univ., Milton Keynes, UK (E. Motta,
J. Domingue, M. Eisenstadt). Goal: using agent approach for Grid
services and collaboration.
§ Start.
2020: Coordinator of Informatics axe at MISTEA (7
permanents, 1 invited researcher, 18 persons total). As “coordinator” I am
mostly representing the team in the institute governance bodies and take over
some global responsibilities:
o
Since
2022: REU (Research Unit contact point for European project).
o
Since
2022: Representation of MISTEA in U. Montpellier’s MIPS Pole.
o
Since
2023: INRAE working group for the 2nd strategical objective of
INRAE’s Data Plan.
§ 2019-2020:
Co-head of FADO research group at
LIRMM with Pr. A. Laurent (6 permanents,
10-12 persons total). I was mostly representing the team in the lab governance
bodies (team councils, informatics department, doctoral school).
§ 2019-2023: Head of ANR D2KAB’s
steering committee (12 persons) as project coordinator.
§ 2017-2019: Co-chair of the ‘ontology
metadata’ task group of the RDA Vocabulary and Semantic Services
Interest Group (15-20 persons).
§ 2012-2024: (Co)supervision of 27+ MSc. Students, 5 PhD, 8 postdocs, 7 engineers
detailed after.
§ 2010-2013: Organizer of the group of interest Web Science Montpellier Meetup (with a series of events).
Missions & Expertise
§ 2024: Reviewer of J. Andersen’s PhD
manuscript, INSA Lyon, May 2024 (inv P. Lamarre & S. Cazalens)).
§ 2023: Reviewer of F. Loffler’s PhD
manuscript, Jena University, June 2023 (invited by B. Konig-Ries).
§ 2022-2023: Member of the COER
(Research Evaluation COmmittee) of ExpoSUM.
§ 2021 & 2022: Vice-President
French ANR expert committee in Artificial Intelligence (CE23).
§ 2022: Member of the Crop Ontology
Strategy Advisory Committee.
§ 2020-2024: French Digital
Agriculture Convergence Institute (DigitAg) Evaluation Committee.
§ Project proposal reviewing and evaluation for French ANR (*3) and US NIH
(*1).
§ Jury member for permanent
researcher/engineer hiring at IUT Béziers (2014), INRAE (2020, 2024), CIRAD
(2022).
§ 2020: Reviewer of O. Alqawasmeh’s
PhD manuscript, Saint-Etienne, Sept. 2020 (invited by M. Lefrancois).
§ 2019: Examiner in A. Laadhar’s PhD
defense, IRIT, Toulouse, Sept. 2019 (invited by O. Teste).
§ 2013: French-US bioinformatics collaboration committee member, supervised
by A. Viari (INRIA) for the Ministries of Higher Education & Research
and Foreign Affairs.
§ 2011-2015: Member of the expert pool of the French Ministry of Higher
Education & Research for evaluating research & development tax credit
(French CIR and JEI).
§ Article rewiewing activity for 16
international journals, 25 different international workhop or conference series
& 8 national workshop or
conference series. Detailled after.
Teaching & Other Responsibilities
§ 2012-2015: Member of Univ. of Montpellier’s council for Information and Communication
Technologies in Education (TICE). Representative for Polytech Montpellier.
§ 2012-2015: Head of Polytech Montpellier iPad for
students project. I ‘led’ a group of 70 teachers interested in pedagogical innovations
using ICT and iPad, in and out of the classroom.
§ 2012-2015: Responsible of the last year of the “Informatics & Gestion”
curriculum at Polytech Montpellier Engineering School (eq. Master degree).
§ 2004-2005: Elected representative of
computer science PhD students at LIRMM. Interesting activity to understand the
organization and operation of a research lab.
Supervision of Research Activities
§ 2024: Supervision & management of
B. Kihal (engineer, AgroPortal).
§ 2024: Co-supervision of I. E.
Bourouche (eng. students, D2KAB) with S. Bouazzouni.
§ 2023-2026: Co-supervision of O. Mechhour,
PhD candidate, (#DigithAg, HE InterCropValues) with M. Roche and S. Auzoux.
§ 2023-2025: Supervision &
management of N. Grau (research & project management, FAIR-IMPACT).
§ 2023-2024: Supervision &
management of S. Mhedhbi (engineer, AgroPortal).
§ 2023: Co-supervision of H.
Djebabria, Z.E. Haddad, B. Kihal (eng. students, D2KAB) with S. Bouazzouni.
§ 2022-2023: Co-supervision of R.
Salazar (postdoc, DACE-DL project) with D. Symeonidou.
§ 2022: Supervision of A. Juan (eng.
Student Epitech Montpellier).
§ 2022: Co-supervision of M. Bouchnaf
and W. Abidi (eng. student, INP-ENSIMAG) with S. Bouazzouni.
§ 2021-2025: Supervision &
management of S. Bouazzouni (engineer, D2KAB & OntoPortal).
§ 2021-2024: Co-supervision of B. Darnala, PhD candidate, (CIFRE, SME Elzeard) with K. Todorov & F. Amardeilh
on machine learning and semantics approaches for agroecology knowledge graphs.
§ 2021: Supervision of S. Bouazzouni
(eng. student, D2KAB).
§ 2021: Supervision of N. Lamrabet
(eng. student, D2KAB) with E. Amdouni.
§ 2020-2021: Supervision of A. Guissé
(visiting scholar, D2KAB).
§ 2020: Supervision of L. Sardois
(eng. student, D2KAB) with A. Castelltort.
§ 2020: Supervision & management of
J. Lamarque (engineer, D2KAB).
§ 2019-2021: Supervision of E. Amdouni
(postdoc, D2KAB).
§ 2019-2020: Supervision of A. Laadhar
(postdoc, D2KAB).
§ 2019: Supervision of
M. Mirzapour (postdoc,
PractiKPharma).
§ 2018-2019: Supervision of
E. Abrahao (postdoc, AgroPortal
project) with K. Todorov & P. Neveu.
§ 2017: Co-supervision of
S. Zevio (MSc student, U. Montpellier) with S. Bringay &
A. Tchechmedjiev.
§ 2017: Supervision of C. Goehrs
(MD & MSc. Student, U. of Bordeaux).
§ 2016-2017: Supervision of
A. Abdaoui (postdoc,
PractiKPharma).
§ 2016-2018: Co-supervision of
A. Tchechmedjiev (postdoc,
PractiKPharma) with S. Bringay.
§ 2016: Co-supervision of
S. Eholié (MSc student, U. of Nantes) with S. Bringay &
M-D. Tapi-Nzali.
§ 2015-2018: Co-supervision of A. Annane, PhD candidate, (cotutelle, Eiffel fellow) with Z. Bellashene
& F. Azouaou (ESI Algeria)) on ontology alignment (SIFR &
PractiKPharma).
§ 2015: Co-supervision of C. El
Ghandour & M. Serhani (MSc students, U. Montpellier) with
J-A. Lossio on prototyping BioTex in SIFR BioPortal.
§ 2015-2018: Supervision &
management of A. Toulet (research engineer, AgroPortal).
§ 2015-2017: Supervision &
management of V. Emonet (research engineer, SIFR).
§ 2015: Supervision of J. Diener
(research engineer, IBC project) with P. Larmande.
§ 2014: Co-supervision of P. Burc
and O. Duplouy (MSc students, U. Montpellier) with S. Harrispe (LGI2P,
Nimes) on semantic distances.
§ 2014: Co-supervision of
L-H. Méric (eng. student, IMT St Etienne) with P. Lemoisson and
G. Surroca.
§ 2014: Supervision of S. Melzi
(MSc student, U. Montpellier).
§ 2014: Co-supervision of A. Dia
(MSc student, U. G. Berger, Senegal) with P. Lemoisson and
G. Surroca.
§ 2013: Co-supervision of K. Cauchois
(MSc. student, U. Rouen) with S. Darmoni (CHU Rouen) on exporting HeTOP’s
content to OWL.
§ 2013-2017: Co-supervision of G. Surroca, PhD candidate, with P. Lemoisson and S.A. Cerri, on
graph-based social/semantic data knowledge representation with Viewpoints.
§ 2013: Supervision of
K. Bouarech, (MSc student, U. Montpelier).
§ 2012-2015: Co-supervision J-A. Lossio-Ventura, PhD candidate, with M. Roche and M. Teisseire on
biomedical terminology extraction (SIFR).
§ 2010: Co-supervision of R. Castro
& B. Paiva (MSc students, U. Montpellier), with S.A. Cerri
(collaboration Stanford-LIRMM) on semantic distances and web service
composition.
§ 2010: Supervision of T. Tenneti
(MSc student, Stanford) on concept recognition.
§ 2009: Co-supervision of A. Ghazvinian
(MSc student, Stanford) with N. Noy on ontology alignment.
§ 2009: Co-supervision of G. Parai
(MSc student, Stanford) with N. Shah on lexicon building.
§ 2009: Co-supervision of N. Bhatia
(MSc student, Stanford) with N. Shah on concept recognition.
§ 2006: Co-supervision of
F. Duvert (MSc student, U. Montpellier), with S.A. Cerri agent-grid
ontology.
§ 2005: Co-supervision of a group of 3
BSc. Students (U. Montpellier) with R. Colleta on web service and
constraint programming.
§ 2005: Co-supervision of a group of 3
BSc. Students (U. Montpellier) with S. Cerri on STROBE & MadKit.
Program chairing and Organization
§ Steering committee 1st FAIR principles for Ontologies and
Metadata in Knowledge Management (FOAM), a new workshop merging Onto4FAIR, CMOMM4FAIR and FOHTI.
§ Organization of D2KAB final event
and public meeting, Montpellier & Online, June 2024 (40 participants).
§ Co-organization of the PhenoHarmonIS Workshop 2024, Montpellier, May 2024 (90
participants).
§ Co-organization of the OA2 meeting
at the 2024 EOSC Winter School.
§ Co-organization of the FAIR-IMPACT Open Call of Support –
FAIRness Assessment Challenge, Online, Oct-Nov. 2023 (25
participants).
§ Co-organization of the FAIR-IMPACT Semantic Artefact
Governance workshop, Sept. 2023, Lecce and online (40 participants).
§ Co-organization of the 2nd
OntoPortal Workshop, Sept. 2023, Lecce (25 participants).
§ Co-organization of 2nd
and 3rd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR), July & Sept. 2023, at FOIS 2022, Sherbrooke, Canada &
SEMANTICS 2022, Leipzig, Germany (20 participants).
§ Co-organization of the FAIR-IMPACT Workshop of Why Mappings
Matter and how to make them FAIR?, April 2023, Online (80
participants).
§ Co-organization of the FAIR-IMPACT Synchronisation Force 2022, Session 4 Metadata, semantics and
interoperability, Online, Nov. 2022 (57 participants).
§ Organization of the 1st
OntoPortal Workshop, Sept. 2022, Montpellier (20 participants).
§ Organization of the 3rd
D2KAB-FooSIN FAIRness assessment AgroHackathon in Aug. 2022 (25 competitors, 6
coaches).
§ Co-organization of 1st Workshop
on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR), Sept. 2022, at Semantics 2022, Vienna, Austria.
§
§ Co-organization of the Biodiversity and Ecology track at OAEI 2020. 7 competitors.
§ Organization of the 2nd IBC-NUMEV
AgroHackathon in July 2017, 15 participants.
§ Organization of the 1st
IBCNUMEV AgroHackathon in June 2016, 30 participants.
§ Co-chair of Semantics for Food, Agriculture, Environment and Nutrition workshop
(SemFAEN 2018) at Semantics 2018, Sept. 2018,
Vienna, Austria.
§ Co-session chair Semantics for biodiversity and ecosystem
research at ICEI 2018.
§ Co-program chair and organization committee of 2nd Int. Workshop on Semantics for Biodiversity
(S4BIODIV 2017) at ISWC 2017, Nov. 2017,
Vienna, Austria. ~30 participants.
§
§ Co-program chair (with D. Cassagne) of the “return of experience”
track of the French ICT in Education
Conference (TICE 2014), Nov. 2014, Beziers, France. ~100 participants.
§
§
§
2010-2013: Organization
of 1st Web Science Montpellier Meetup workshop in Montpellier, France, May 13th 2011. 25
participants. Other smaller events have followed.
§ Participation to the organization of
local workshops (OTM 2006 & ALCAA 2004).
Article Reviewing
Database (Oxford Academic), Data Intelligence (open access), Semantic Web Journal (IOS Press), Applied Ontology (IOS Press), Journal of Web Semantics (Elsevier), Bioinformatics (Oxford Academic), BMC Bioinformatics (BioMed Central), Knowledge-Based Systems (Elsevier), Journal of Biomedical Informatics (Elsevier), Journal of Biomedical Semantics (BioMed Central), Access (IEEE), IMIA Year Book (Schattauer), French Technique et Science Informatique (Hermès), French Revue d'Epidémiologie et de Santé
Publique (Elsevier), Service Oriented Computing and
Applications journal (Springer), Grid Computing and Multi-Agent Systems journal
(Serials Publications)
International Program Committees
§ Int. Conference on Knowledge
Engineering and Knowledge Management (EKAW 2020, 2022, 2024).
§ 1st Workshop on
Controlled Vocabularies and Data platforms for Smart Food Systems (SmartFood
2023).
§ International Conference on
Biomedical Ontology (ICBO 2022).
§ 1st-3rd Int. Workshop on Semantics
for Biodiversity (S4BIODIV 2013, 2017,2021).
§ International Conference on Formal
Ontology in Information Systems (FOIS 2021, 2023, 2024).
§ International Symposium on
Information Management & Big Data (SIMBig 2014-2021).
§ International World Wide Web
Conference (WWW 2018-2019, WWW 2012 (Demo track))
§ International Semantic Web
Conference (ISWC 2017-2018, 2023, 2024).
§ European/Extended Semantic Web
Conference (ESWC 2017, 2019, 2020, 2023).
§ European Federation for Information
Technology in Agriculture, Food & Environment (EFITA 2017).
§ 1st Language, Data and Knowledge
conference (LDK 2017)
§ 11th-18th BioOntologies SIG (BioOntologies
2009-2017).
§ Semantic Web Applications and Tools
for Life Sciences (SWAT4LS 2015-2016-2018, 2023).
§ 11th &12th African Research in
Computer Science and Applied Mathematics (CARI 2014-2016)
§ 1st Computational Semantics in
Clinical Text (CSCT 2013) workshop
§ 4th Int. Conference on Web Science (WebSci 2012).
§ 1st & 2nd Int. Workshop on Web
Science & Information Exchange in Medical Web (MedEx 2010-2011).
§ 9th, 11th & 13th Int. Conference
on Intelligent Tutoring (ITS 2008, ITS 2014, ITS 2012).
§ 4th & 5th Int. KES Symposium on Agents
& MAS Technologies & Applications (AMSTA 2010-2011).
§ Workshop on Ontology Repositories
for the Web (SERES 2010).
§ 1st Int. Workshop on User-generated
Services (UGS 2009).
§ Workshop Extending Database
Technology for Life Sciences workshop (EDTLS 2009).
§ Int. Workshop on Service-Oriented
Computing: Agents, Semantics, and Engineering (SOCASE 2009).
National Program Committees
§ 23ème conférence francophone sur l’Extraction et la Gestion des Connaissances (EGC 2023).
§ Journées francophones d’Ingénierie des Connaissances (IC 2013-2024).
§ 1er & 2ème Atelier Web des données (AWD 2019, 2020).
§ Workshop Knowledge Engineering &
Health (IA & Santé 2018-2021, SIIM 2015-17, ICSanté 2012-2016).
§ Workshop sources & data
integration in agriculture, food, environment ontologies (IN-OVIVE 2017)
§ 6èmes Journées francophones sur les Ontologies (JFO 2016).
§ 1er Atelier Ontologies et Jeux de Données pour évaluer le web sémantique (OJD 2012).
§ 1er-3ème Atelier Quantité et Robustesse pour le Web de données (QetR 2011-2013).
§ 1er Atelier Extraction des Connaissances et Contextualisation (ExCoco 2011).
§ 7ème Colloque Agents Logiciels, Coopération, Apprentissage, Activité (ALCAA 2004).
The
first author is always the “main” author. The last author is generally the
supervisor. Most of publications or communications (166 total) have been
peer-reviewed (if not explicitly mentioned), including:
§ 29 journal (6 as first author, 4 as second
author, 4 as last author).
§
77 articles in international
conferences (32), international workshops (20) or
national (French) conferences (25) all with proceedings.
§
33 posters or demos in
international venues.
§
§ 7 publications are the result of a
working group (e.g., RDA), or a community paper.
Overall,
my publications cumulate 4200 citations as
of Google Scholar (June 2024); including +1200 citations for publications as
first author. Evolution of my citations (as of Google Scholar) is given aside.
Publication
context and domains
§ Biomedical Informatics: 2 recent
articles in Journal of Biomedical Informatics
(Elsevier, IF 6.32), 4 articles in BMC
Bioinformatics (IF 3.24, CORE A) cumulating
332 citations, 1 in Nucleic Acids
Research (Oxford, IF 10.16) with 1145
citations, 2 application notes in Bioinformatics
(Oxford, IF 6.94), 2 articles (one
with 363 citations) at AMIA Symposiums which is one of the best
venues to publish in this field. 2 articles (one with 109 citations)
in BMC Biomedical Semantics (IF 2.41).
§ Semantic Web: 3 articles & 4 posters/demos (all
cumulating 241 citations) in Int. Semantic Web Conference (CORE A),
the main conference in the domain or 2 articles in EKAW another important
conference. Plus, the 1st prize at the 2010 Semantic Web Challenge and
a corresponding publication (124 citations)
in Journal of Web Semantics (Elsevier,
IF 2.76). One awarded paper at Web Science Conference.
§ NLP, text mining & information
retrieval: 4
conferences or workshop articles related to text mining and language in
biomedicine (LREC’16, PolTAL’14, IDEAS’14,
JADT’14, LBM’13). One article in Information
Retrieval (Springer, IF 2,29) with 76
citations and one in Knowledge Discovery in Bioinformatics (IGI
Global) both on terminology extraction.
§ Agronomy & agriculture: multiple
poster-demos and workshop papers recently published in this new field of
application. One article as first author in Computers
and Electronics in Agriculture (Elsevier, IF 5.57) with 92 citations. Two group articles in
prestigious journals: Database
(Oxford, IF 3.45) and PLoS One (PLoS,
3.24). One recent chapter in a book in the Series
in Agricultural Science (Burleigh Dodds).
§ Distributed systems: 1 article in the reference journal
for the topic of agent-grid integration, Multiagent
and Grid systems (IOS Press, CORE B) as well as 1 article in the Int. Workshop on Service-Oriented Computing:
Agents, Semantics, and Engineering. Plus 1 article in Applied Artificial Intelligence (Taylor & Francis, IF 1.17,
CORE B) with 27 citations.
§ French
conferences: Such as Journées
francophones d’Ingénierie des Connaissances, or d’Informatique médicale or du Traitement
Automatique des Langues Naturelles, or sur
les Systèmes Multi-Agents, or des
Ontologies or de Recherche
d’Information et Applications. 11 French publications (over 24) are direct French versions of English
papers; others are usually preliminary work.
Six
Selected publications
Hereafter,
underlined names are co-authors who worked under my supervision.
§ [CJ5] Andon Tchechmedjiev, Amine Abdaoui, Vincent
Emonet, Stella Zevio, and Clement Jonquet. SIFR Annotator: Ontology-Based Semantic Annotation
of French Biomedical Text and
Clinical Notes. BMC Bioinformatics,
19:405–431, December 2018. 12 citations.
https://dx.doi.org/10.1186/s12859-018-2429-2
This paper is one of the main
results of the SIFR project: it is the presentation and evaluation of the SIFR
Annotator. This work originally founds its source in my postdoctoral research
activity when I work on semantic annotation.
§ [CJ8] Clement Jonquet, Anne Toulet, Biswanath Dutta, and Vincent Emonet. Harnessing the power of unified metadata in an ontology repository: the case of AgroPortal. Data Semantics, pages 1–31, August 2018. 13 citations.
https://dx.doi.org/10.1007/s13740-018-0091-5
This journal paper synthetizes our
work on ontology metadata between 2016 and 2018. It presents an analysis of
practices, then a unified ontology metadata model and its implementation and
exploitation in the AgroPortal ontology repository.
§ [CJ13] Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé-Yeumo, Vincent Emonet, John Graybeal, Marie-Ange´lique Laporte, Mark A. Musen, Valeria Pesce, and Pierre Larmande. AgroPortal: an ontology repository for agronomy. Computers and Electronics in Agriculture, 144:126–143, January 2018. 92 citations.
https://dx.doi.org/10.1016/j.compag.2017.10.012
This journal paper presents
AgroPortal, along with its original driving use cases and early adopters. It is
a perfect index to work done in this project on ontology metadata, mappings,
annotation, etc. This paper and the four poster-demo articles about AgroPortal
cumulates today 134 citations.
§ [CJ18] Clement Jonquet, Paea LePendu,
Sean Falconer, Adrien
Coulet, Natalya F. Noy,
Mark A. Musen, and Nigam H. Shah. NCBO Resource Index: Ontology-Based
Search and Mining of Biomedical Resources. Web Semantics, 9(3):316–324, September
2011. 1st prize of Semantic Web Challenge
at the 9th Int. Semantic Web Conference,
ISWC’10, Shanghai, China. 124 citations.
https://dx.doi.org/10.1016/j.websem.2011.06.005
This journal paper is one of the
main results of my postdoc. It was my first contact with big biomedical data,
establishing a semantic index for a large number of continuously evolving datasets
and ontologies. Even if not explicitly used anymore, the NCBO Resource Index
illustrated the challenges of ontology-based indexing at large scale as
acknowledged by the 1st price at the Semantic Web Challenge
organized at ISWC 2010. The three publications on this topic cumulate 322
citations.
§
[CJ22]
Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael
Dorf, Nicholas B. Griffith, Clement
Jonquet, Daniel L. Rubin, Margaret-Anne Storey, Christopher G. Chute, and Mark A. Musen. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research, 37(web server):170–173, May 2009. 955 citations.
https://dx.doi.org/10.1093/nar/gkp440
This journal paper is the reference
paper for the NCBO BioPortal ontology repository. The portal is now the most
comprehensive and largely used ontology and terminology repository in
biomedicine.
§ [CJ47] Clement Jonquet, Nigam H. Shah, and Mark A. Musen. The Open Biomedical Annotator. In American Medical Informatics Association Symposium on Translational BioInformatics, AMIA-TBI’09, pages 56–60, San Francisco, CA, USA, March 2009. 311 citations.
https://hal.archives-ouvertes.fr/hal-00492024
This conference article was the
first paper presenting the NCBO Annotator, the implementation of the
methodology designed during my postdoc for annotating textual data with
ontology concepts. The three publications on the NCBO Annotator cumulate today
567 citations.
Training
& tutorial events
§ Horizon Europe FAIR-IMPACT FAIRness Assessment Challenge, Oct.-Nov. 2023.
§ LifeWatch Semantic Academy, Lecce, Sept. 2023 (invited by N.
Fiore).
§ 9th EGC Winter School 2023, Lyon, Jan. 2023 (invited by C.
Faron-Zucker).
§ Int. SemTech training workshop, ISI, Bangalore, Feb. 2021 (invited by B. Dutta).
§ ENVRI-FAIR First training event, Dresden, Feb. 2020 (invited by M. Hellström).
§ LifeWatch/ENVRI Plus Data FAIRness Int. Summer school, Lecce, July 2019 (invited by N.
Fiore).
§ Lecture on ontology-based services,
DECOL Master, U. Montpellier (invited by F. Ulliana), April 2019.
§ E-ENVIR CNRS thematic school, Gif-sur-Yvette, Oct. 2019 (invited by C.
Martin).
§ Tutorial on ontology management
& services, CNRS INIST, Nancy, Dec. 2017 (invited by C. Francois).
§ Tutorial SIFR BioPortal & AgroPortal, ontology management &
services, IC 2016, Montpellier, June. 2016.
§ Tutorial on the use iPad in
education at Forum TIC’s, Mons, April 2015 (invited by B. Champagne).
Scientific
Seminars & Invited talks
§ PhenoHarmonIS, May 2024 (invited by E. Arnaud).
§ Embrapa sede seminar, Brazilia,
April 2024 (invited by M. Telles).
§ GO-FAIR Agro Brazil network seminar,
Oct. 2023 (invited by M. Telles).
§ INRAE Semantic Linked Data, Cap d’Agde, Oct. 2023 (invited by.
P. Neveu & P. Buche).
§ EOSC Symposium FAIR, Data Quality Management and
Research Metrics Assessment, Madrid, Sept. 2023 (invited by C. Schubert).
§ 6th Annual AGROVOC
Editorial Community Meeting, Freising, July 2023 (invited by I. Subirats).
§ Horizon Europe TITAN project
webinar, July 2023 (invited by P. Neveu).
§ H2020 OntoCommons 2nd Global Workshop, June 2023 (invited by J. Breslin)
§ IEA Wind Task 43 Metadata Challenge Webinar Series, June 2023 (invited by S. Barber).
§ Fusion group meeting, Jena
University, June 2023 (invited by B. Konig-Ries).
§ BBOP group meeting, UC Berkeley,
April 2023 (invited by Chris Mungall).
§ Musen’s lab meeting, Stanford
University, March 2023 (invited by M. Musen).
§ CGIAR Ontologies Community of Practice Webinar, Oct. 2022 (invited by E. Arnaud).
§ 4th Educational Series on Applied Ontology (ESAO) seminar, Oct. 2022 (invited
by C. Trojhan).
§ 12th Int. Workshop on Formal Ontologies
meet Industry
(FOMI22), Sept. 2022 (invited by Y. LeFranc).
§ BioPortal group meeting, Stanford,
April 2022 (invited by J. Graybeal).
§ H2020 OntoCommons Workshop on Addressing challenges of the
Industry 5.0, Nov.
2021 (invited by J. Breslin).
§ INRAE Inter-CATI meeting “Semantic
Linked Data”, Sète, Oct. 2021 (invited by P. Neveu and P. Buche).
§ H2020 FAIRsFAIR Common Minimum Metadata for Semantic
Artefact, June
2021 (invited by Y. Le Franc).
§ H2020 OntoCommons Workshop on Tools for Ontology Engineering, March 2021 (invited by M. d’Aquin).
§ Occitanie Data seminar, Jan. 2021
(invited by E. Clement).
§ MISTEA research seminar, Montpellier, Dec. 2020 (invited by
P. Neveu).
§ Int. FAIR Convergence Symposium session “FAIR Digital Objects
for Cross-domain Data Searching & Linking and Semantic Interoperability”,
Dec. 2020 (invited by P. Mutschke).
§ MADICS AGEE (AGriculture, Environment, Ecology)
workshop, July 2020 (invited by S. Bimonte).
§ Agronomy & AI thematic day, French conference on AI, July 2020
(invited by. T. Guyet and D. Rousseau).
§ RDA Agricultural Data Interest Group
(IGAD) meeting, May
2020 (invited by I. Subirats)
§ OntoPortal Alliance kick-off
meeting, May 2020 (invited by J. Graybeal).
§ H2020 FAIRsFAIR Minimum Metadata for semantic
artefacts workshop, April 2020 (invited by Y. Le Franc).
§ AquaDiva BioGeo-Colloquium, Jena
University, Nov. 2019 (invited by B. Konig-Ries).
§ Keynote at Int. Symp. on Integrative Bioinformatics, Paris, Sept 2019 (invited by C.
Pommier).
§ Talk at MSCA monitoring meeting on
e-health and biomedical technologies, Brussels, June 2019.
§ Invited talk at Meteo France thematic day on data authorities, Toulouse, April 2019 (invited by
P. Dayre).
§ LIRMM scientific day, Montpellier,
Dec. 2018 (invited by P. Poignet).
§ RDA France 1st National Day, JNSO 2018, Paris, Dec. 2019
(invited by F. Genova).
§ INRIA’s Wimmics seminar, Inria
Sophia-Antipolis, Nov.2018 (invited by F. Gandon).
§ PhenoHarmonIS workshop, Montpellier,
May 2018 (invited by E. Arnaud).
§ RDA 11th Plenary, IGAD
pre-meeting, Berlin, March 2018 (invited by I. Subirats).
§ H2020 EUDAT Conference Semantic
Working Group, Porto, Jan. 2018 (invited by Y. Le Franc).
§ Keynote INIST ‘Ingénierie des Connaissances’ Series, Nancy, Dec. 2017 (invited by C. Francois).
§ IC-Foods Conference, UC Davis, Nov. 2018 and 2017 (invited by M.
Lange).
§ Keynote at SIMBig 2017, Lima, Sept. 2017 (invited by J-A. Lossio).
§ GDR SemanDiv, Montpellier, July 2017
(invited by E. Garnier).
§ French Minister – DSSIS (serveurs multi-terminologiques), Paris, June 2017 (invited by B. Séroussi).
§ BMIR Research in progress
colloquium, Stanford Univ., May 2016 (invited by M. Musen).
§ Protégé group meeting, Stanford Univ., April 2016
(invited by T. Tudorache).
§ Dumontier’s lab group meeting,
Stanford Univ., Jan. & Nov. 2016 (invited by M. Dumontier).
§ Keynote at the French RISE 2015
workshop, Rennes,
June 2015 (invited by C. Roussey).
§ Protégé group meeting, Stanford, April 2015 (invited by
T. Tudorache).
§ Keynote at Forum TIC’s, Mons, April
2015 (invited by B. Champagne).
§ LGI2P science & society seminar,
Nimes, March 2015 (invited by S. Harispe).
§ CENTAL team at UC Louvain, Dec. 2014
(invited by C. Fairon).
§ Réseau IN-OVIVE, INRA, Montpellier,
Oct. 2014 (invited by P. Neveu).
§ IBC Scientific day, Montpellier, May
2014 (invited by O. Gascuel).
§ SPIM team seminar at INSERM Paris,
June 2011 (invited by M-C. Jaulent).
§ LIM team seminar at Rennes Univ.,
April 2011 (invited by O. Dameron).
§ CISMeF team seminar at Rouen School
of Medicine, March 2011 (invited by S. J. Darmoni).
§ Research seminar on ICT &
Health, LIRMM, Montpellier, February 2011.
§ EXMO team seminar at INRIA Grenoble,
March 2010 (invited by J. Euzenat).
§ Smile team seminar at LIRMM, Univ.
Montpellier, Feb. 2009 (invited by S. A. Cerri).
§ EDELWEISS team seminar at INRIA
Sophia-Antipolis, Jan. 2009 (invited by F. Gandon).
§ Talk at the NCBO developer conference,
Stanford Univ., USA, Dec. 2007.
§ Intelligent Interactive Distributed
Syst. group, Vrije Univ., Amsterdam (invited by F. Brazier). May 2007.
§ LIRMM's Informatics department day, UM2, France. July 2005.
§ Protégé group meeting, Stanford Univ., CA, USA (invited by M. Crubezy). June
2005.
§ E-LeGI WP6 (Work Package 6) seminar, LIRMM, UM2, France. June 2004.
§ Computer Science PhD students seminar, LIRMM, UM2, France. January 2004.
§ Talk within the GT MFI (Modèles
Formels de l'Interaction) working group, LIP6, Univ. Paris 6, Dec. 2003.
§ Social Informatics seminar, LIRMM,
Univ. Montpellier (invited by S. Cerri). June 2003.
§
§ Teacher at Polytech Montpellier Engineering
School. My teaching
activities were paused from 2015 to 2020 during my mobility and the return
phase of my H2020 MSCA project at Inria.
§ 2012-2015: Polytech Montpellier iPad for students project. I run a working group of
70 teachers interested in pedagogical innovation using ICT and iPad, in and out
of the classroom.
§ Preparation of lectures/tutorials/technical
work, evaluation tasks (exam, corrections, jury), projects and internships
management, administrative responsibilities. Some classes in English from 2010
to 2012.
§ Around 20 days of miscellaneous
teacher training followed (pedagogy, numeric, reverse teaching, etc.)
§
§ Lectures: Structure and Interpretation of Computer Programs, introduction to algorithmic and
programming with Scheme/Mapple, French Informatics and Internet
Certificate
(Open/MS Office, e-learning platforms, etc.), Internet languages (HTML,
Java/Javascript, PHP, etc.), Computer Architecture (representation, CPU/Memory, MIPS
language), Algorithmic & Programming (ADA, basic algorithmics, data
structures), Internet Application and
Interoperability
(Web application architectures, Web technologies, XML, Web services, J2EE,
.NET), Semantic Web (Ontologies 101, technologies &
languages, applications).
§ Internship supervision: technical BSc. (mathematics & computer
science), MSc students in computer science.
§ Programming languages:
functional/applicative (Lisp, Scheme) or object-oriented (Java) or imperative (Ada,
Maple). Some knowledge of MIPS assembler.
§ Java & JEE framework technologies
(JDBC, Spring, Eclipse).
§ Service Oriented Architectures and
Web applications. Web services in SOAP/WSDL (Axis) & REST.
§ Biomedical terminologies and
ontologies (SNOMEDCT, MeSH, UMLS, OBO, etc.) as well as Semantic Web
technologies (RDF/OWL/SKOS/SPARQL).
§ Database systems (SQL), MySQL/JDBC
and information system modeling language (UML, BPMN).
§ Web languages & technologies
(XML, HTML, Javascript, CSS, PHP/MySQL, JSON).
§ Distant learning / e-learning
platforms e.g., WebCT, Claroline, Moodle.
§ MadKit multi-agent platform
(developed within the SMILE team at LIRMM).
§ Experiences in several associations
(student, sportive, social). Summer jobs from 1996 to 2002 in agriculture and
wineries.
§ Music, travelling (several trips in
Europe, America, South America and Asia.), reading (novel and press).
§ Rock climbing (indoor/outdoor) and
other outdoor sports (mountaineering, ice-climbing, hiking, etc.).
§ French: first language.
§ English: very good (school &
working knowledge), lived 6 years in the USA.
§ Spanish: a few skills (from school).
§ Strong international orientation of
work (publications & thesis/HDR manuscripts written in English,
international PhD/HDR defense jurys, international postdoc).
§ Dr. Pascal Neveu, INRAE – MISTEA – pascal.neveu@inrae.fr
§ Pr. Anne Laurent, University of
Montpellier – LIRMM – laurent@lirmm.fr
§ Dr. Fabien Gandon, Inria
Sophia-Antipolis – Wimmics – fabien.gandon@inria.fr
§ Pr. Stefano A. Cerri, University of
Montpellier – LIRMM – cerri@lirmm.fr
§ Pr. Mark A. Musen, Stanford
University – BMIR – musen@stanford.edu
§ Pr. Nigam H. Shah, Stanford
University – BMIR – nigam@stanford.edu
Defense and Jury
Title: Ontology repository
and Ontology-based Services – Challenges, contributions and applications to
biomedicine & agronomy
Discipline: Informatics, I2S
doctoral school, University of Montpellier
Manuscript: https://tel.archives-ouvertes.fr/tel-02133335
Defense: May 28th 2019
Jury: Michel Dumontier (professor), Maastricht University (reviewer)
Nathalie
Aussenac-Gilles (DR CNRS), CNRS, Toulouse (reviewer)
Mathieu
D'Aquin (professor), Nat.
Univ. of Ireland, Galway (reviewer)
Fabien
Gandon (DR
INRIA), INRIA Sophia Antipolis (examiner)
Juliette
Dibie-Barthélemy (professor), AgroParisTech, Paris (examiner)
Pascal
Poncelet (professor), University of Montpellier (examiner)
Mark
A. Musen (professor), Stanford University (invited)
Stefano
A. Cerri (prof.
emeritus), University of Montpellier (invited)
Abstract
With the explosion of the number of ontologies and vocabularies
available in the semantic web, ontology libraries and repositories are
mandatory to find and use them. Their functionalities span from simple ontology
listing with metadata description to rich platforms offering various advanced
ontology-based services: browse, search, visualization, metrics, annotation,
recommendation, data access, etc. Studying ontology repositories opens then a
wide spectrum of informatics research questions in areas such as knowledge
representation, semantic web, data integration, natural language processing,
ontology alignment and more. Ontology repositories are usually developed to
address certain needs and communities. BioPortal, the ontology repository built
by the US National Center for Biomedical Ontologies is the most important
resource in biomedicine. It relies on a domain independent open technology that
we have contributed to build (at Stanford) and extensively reused and extended
for our research (at University of Montpellier) and applications to biomedicine
and agronomy.
In this manuscript, we present and discuss six high level challenges for
ontology repositories and services: (i) standardize and extend metadata
used to describe ontologies and use these metadata to facilitate ontology
evaluation, identification and selection; (ii) multilingualism, which
requires rethinking ontology repositories to embrace (and encourage) the
multilingual semantic web; (iii) all issues related to ontology alignment,
not just the automatic generation of mappings, but also their extraction, storage,
validation, etc., (iv) the design of better and new generic ontology-based
methods especially for processing free text data, (v) the use of
ontologies for semantic annotations & linked data; and finally,
(vi) scalability & interoperability of the different semantic
resources management platforms. For each challenge, we describe and point to
results obtained in the context of our ontology repository projects over the
last 12-years, especially the NCBO, SIFR, PractiKPharma and AgroPortal
projects. We believe our results illustrate potential solutions to move forward
in this domain of research.
FAIR-IMPACT is a Horizon Europe funded CSA project which focuses on
expanding FAIR solutions across the EOSC. It builds on the results of FAIRsFAIR
and other relevant projects and initiatives. FAIR-IMPACT will identify proven
domain solutions and facilitate the interoperable uptake of these solutions
across scientific domains and for different types of research output. This
includes the overall FAIRification of various research objects from assigning
and managing identifiers, describing them with shared and common semantics to
making them interoperable and reusable, as well as the challenge of projecting
the FAIR principles to other types of research objects such as software.
Scientific communities are included in the consortium as integrated use case
partners. This will ensure that viable and tested solutions from one domain can
be piloted in others and help to achieve wider uptake, adoption, implementation
of, and compliance with the FAIR principles. As the project unfolds, additional
support mechanisms (cascading grants, in-kind support) will be introduced. The FAIR-IMPACT
ambition is to build a web of FAIR data and related services together with the
scientific community and relevant stakeholder groups, and to take steps towards
realising the ambition of a web of Open Science. With its focus on increasing
FAIRness, FAIR-IMPACT contribute to improving public trust and reproducibility
in science.
As work-package leader, I am supervising the different tasks related to
ontologies and metadata in the project.
Information System to explore the agronomic and oenological potential of
vine genotypes (VitisExplorer)
Trials for the evaluation of genotypes resulting from programs for the
creation of disease-resistant varieties will generate large volumes of data in
the years to come. The objective of the proposed project is 1) to propose
computer architectures and exchange formats that allow a coherent structuring
of these data in order to allow exchanges and comparisons, 2) to develop
user-friendly tools for graphical exploration of these data as well as than
statistical analyzes 3) to acquire tools for fine characterization of the
responses of genotypes to the environment in order to anticipate their behavior
in conditions other than those in which they were evaluated. The VitisExplorer
project, supported by the French PNDV program, gather INRAE Colmar, INRAE
Montpellier and the French Wine and Vine Institute (IFV).
As a partner in the project, I am bringing in expertise on the use of
ontologies in building information systems based on the OpenSILEX suite.
DAta-CEntric AI-driven Data Linking (DACE-DL)
In a world of open science and FAIR data, Linked Data has been gaining
popularity, due to the means they offer for (meta)data exchange, federation and
sharing on the Web. Data linking is the scientific challenge of automatically
establishing typed links between the entities of two or more structured
datasets. A variety of complex data linking systems exists, evaluated on public
benchmarks. While they have allowed for the generation of vast amounts of
linked data in the context of various dedicated projects, data generic systems
often have limited applicability in many real-world scenarios, where data are
highly heterogeneous and domain-specific. DACE-DL targets a paradigm shift in
the data linking field with a data-centric bottom-up methodology relying on machine
learning and representation learning models. Based on current and previous
linked data projects (in music, encyclopedia, agronomy, biodiversity), we will
study what a hybrid AI approach can learn from already available and diverse
linked data and modularized existing data linking systems in order to re-inject
this knowledge into current Web-data challenges, for example in the context of
the COVID-19 crisis or in the agronomy domain.
As a partner in the project, I am involved in MISTEA activities on
classifying linking problem types with the postdoc of R. Salazar.
OntoPortal Alliance (French section)
The OntoPortal Alliance, partially supported by the IRT-NUMEV eponym project,
brings together three partners: LIRMM/MISTEA in Montpellier, BMIR at Stanford
University and LifeWatch ERIC in Italy, who are all working together to
jointly develop methods and a technology, OntoPortal, for the management of
ontologies and ontology-based services. This work is deployed in multiple ontology
repositories in different scientific domains, respectively by partner: agronomy
(AgroPortal), biomedicine (BioPortal) and ecology/biodiversity (EcoPortal).
As the PI of the IRT-NUMEV supported part of the Alliance my job is to
coordinate the French adoptions of the OntoPortal technology and encourage
newcomers. I am also pushing for the adoption of this technology in the context
of the European Open Science Cloud.
French section GO FAIR Food Systems ImplementATION Network (FooSIN)
The objectives of the FooSIN project are to establish and work within
the recently proposed and endorsed GO FAIR Food Systems Implementation Network
(IN) to 1) accelerate the implementation
of FAIR principles in the agri-food community, and 2) position France as a
leader in this evolution and make French actions and productions more visible
at an international level. The Food Systems IN, co-led by INRAE and Wageningen University
and Research, gathers 22 major actors of the agriculture and nutrition domains
worldwide, who commit to FAIR principles and collectively work for their wider
and quicker adoption. As members of the Food Systems IN, we propose concrete
actions towards the French community of people involved in data production and
management for agriculture and food. We will organize a Bring-Your-Own-Data
workshops (a.k.a datathons), seek for adapted training materials, and recommend
tools and methodologies to FAIRify data and semantic resources, with the aim to
leverage the FAIR awareness and skills, and the adoption of efficient tooling
by our community. We will also propose
original tools and services for data FAIRification to be adopted and
disseminated by the Food Systems IN at the international level. These services
and tools may also be transferred to other fields among the INs of the GO FAIR
network.
As a co-principal investigator, I am leading FooSIN’s WP2 on GO BUILD to
establish tools and methodologies related to the use of semantics for food
systems.
Data to Knowledge in Agronomy and Biodiversity (D2KAB)
D2KAB’s primary objective is to create
a framework to turn agronomy and biodiversity data into knowledge –semantically
described, interoperable, actionable, open– and investigate scientific
methods and tools to exploit this knowledge for applications in science &
agriculture. Agronomy/agriculture and biodiversity (ag & biodiv) face
several major societal, economical, and environmental challenges, a semantic
data science approach will help to address. We shall provide the means –ontologies and linked open data– for ag
& biodiv to embrace the semantic Web to produce and exploit FAIR data.
To do so, we will develop new original methods and algorithms in the following
areas: data integration, text mining, semantic annotation, ontology alignment
and linked data exploitation. D2KAB project, supported by French ANR, brings
together a unique multidisciplinary consortium of 12 partners to achieve this
objective: 2 informatics research units (LIRMM, I3S); 6 INRAE/IRSTEA/IRD
applied informatics research units (URGI, MaIAGE, IATE, DIST, TSCF, DIADE)
specialized in agronomy or agriculture; 2 labs in biodiversity and ecosystem
research (CEFE, URFM); 1 association of agriculture stakeholders (ACTA); and 1
partnership with Stanford BMIR department. Each of the project driving scenarios (food packaging,
agro-agri linked data, wheat phenotype, ecosystems & plant biogeography)
will have a significant impact and produce concrete outcomes for ag &
biodiv scientific communities and socio-economic actors in agriculture.
As PI, my contributions are to coordinate the project and monitor the
results of each tasks. I am leading the coordination and dissemination
work-packages as well as WP2 on ontology-based services.
Visa for Text Mining (VisaTM)
Developing and offering Text and
Data Mining (TDM) services for scientists raises several legal,
organizational and scientific questions. The VisaTM project of the French BSN (Bibliothèque Scientifique Numérique – recently
renamed Comité pour la Science Ouverte)
brought together three complementary research organizations to profile an infrastructure for TDM
services in France: INRA, member of the H2020 text and data mining
eInfrastructure project OpenMinTeD (http://openminted.eu),
CNRS-INIST, host of the ISTEX (www.istex.fr) platform
and University of Montpellier (LIRMM) as leader of the AgroPortal project (http://agroportal.lirmm.fr). The
project, divided into 3 work-packages (study, conception, scenarios), allowed
the development of mechanisms to provide data resources (text corpora) and
semantic resources (ontologies/terminologies) to the OpenMinTed infrastructure.
ISTEX (scientific publications databases) and AgroPortal (agronomy related
ontologies) were used as demonstrators.
My contributions, within the “Conception”
work-package, were to enable the automatic consumption of terminologies and
ontologies (from different ontology repositories) within the OpenMinTed
platform.
AgroPortal
Many vocabularies and ontologies are produced to represent and annotate
agronomic data. However, those ontologies are spread out, in different formats,
of different size, with different structures and from overlapping domains.
Therefore, there is need for a common platform to receive and host them, align
them, and enabling their use in agro-informatics applications. By reusing the
National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology
repository for agronomy and related domains. We offer a portal that
features ontology hosting, search, versioning, visualization, comment, and
recommendation; enables semantic annotation; stores and exploits ontology
alignments; and enables interoperation with the semantic web. We
plan to turn that prototype into a real service to the community (http://agroportal.lirmm.fr). We first focused on five driving
agronomic use cases that participated in the design and orientation of the
project to anchor it in the community: RDA Wheat Data Interoperability WG, Crop
Ontology project, INRAE vocabularies, AgroLD and Agrisemantics Map of Agri-food
data standards. By specifically
addressing the requirements of the agronomy community, AgroPortal has kindled
an important interest both at the national and international levels. The
platform currently hosts 124 vocabularies with more than 2/3 of them not
present in any similar ontology repository and 10 private ontologies. We have
identified 90 other candidate ontologies that will be loaded in the future to
complement this valuable resource. The project was originally supported by IBC
& Labex NUMEV & Agro. It will now be supported by D2KAB project.
As coordinator, I have been the principal architect of the project and
the supervisor of 2/3 persons (postdoc and engineer) involved in the
development, maintenance, outreach and curation of the platform.
Practice-based evidences for actioning Knowledge in Pharmacogenomics (PractiKPharma)
Pharmacogenomics (PGx) studies how individual gene variations cause
variability in drug responses. Knowledge in PGx is typically composed of units
that have the form of ternary relationships gene
variant–drug–adverse event –stating that an adverse event may occur for
patients having the gene variant when being exposed to the drug– and can be
formalized to different extents using biomedical ontologies. Most of the state-of-the-art
knowledge in PGx is not yet validated, consequently not yet applicable to medicine.
During the PractiKPharma project our objective was to validate or moderate pharmacogenomics state-of-the-art knowledge on the
basis of practice-based evidences, i.e., knowledge extracted from
Electronic Health Records (EHRs). To achieve our goal, we extracted
state-of-the-art knowledge from PGx databases (PharmGKB) and literature
(PubMed), and we extracted observational knowledge from clinical data; then we
compared knowledge units extracted from these two origins, to confirm or
moderate state-of-the-art knowledge, with the goal of enabling personalized
medicine. PractiKPharma project, supported by French ANR, and head by A.
Coulet, brought together two informatics labs: LORIA (Nancy) & LIRMM
(Montpellier); and two hospitals: HEGP (Paris) and CHU St Etienne. At LIRMM, we
had enhanced the SIFR annotation workflow to capture clinical narrative and
semantically annotate French electronic health records.
My contributions were to drive and supervise LIRMM activities (3
persons) and participate into the research for PGx knowledge modelling and
comparison. Our team main mission was to enhance the SIFR annotation workflow
to capture clinical narrative and semantically annotate French electronic
health records.
Semantic Indexing of French Biomedical Data Resources (SIFR)
Biomedical data integration and semantic interoperability is necessary
to enable new scientific discoveries
that could be made by merging different available data (i.e., translational
research). A key aspect in addressing semantic interoperability for life
sciences is the use of terminologies and ontologies as a common denominator to
structure biomedical data and make them interoperable. The SIFR project, mainly
funded by French ANR Young Researcher and H2020 MSCA programs, proposed to 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. SIFR built an ontology-based indexing workflow (i.e.,
French Annotator) similar to what exists for English resources but dedicated
and specialized for French. We designed the SIFR Annotator (http://bioportal.lirmm.fr/annotator) a web service for semantic
annotation of French textual medical data. SIFR brought together several young researchers
at LIRMM to achieve this objective: Dr. Clement
Jonquet, accompanied by two young assistant professors, Dr. Sandra Bringay
(text/data mining) and Dr. Mathieu Roche (NLP). Plus: (i)°Stanford BMIR, a worldwide leader providing
(English-)ontology-based services to assist health professionals and
researchers in the use of ontologies to design biomedical knowledge-based
systems; (ii)°CISMeF group, which is
the national leader to provide French health terminology-based services.
As PI, my contributions were to coordinate the project and monitor the
results of each tasks (two PhDs, 1 engineer, multiple interns).
Institut de biologie computationnelle (IBC)
This project, supported by Investissement
d’Avenir French ANR program, aimed to develop innovative methods and
software to analyze, integrate and contextualize large‐scale biological data in the fields of health, agronomy and environment. Several branches of research are
combined: algorithmics (combinatorial, numerical, highly parallel, stochastic),
modeling (discrete, qualitative, quantitative, probabilistic), and data
management and information retrieval (integration, workflows, cloud). IBC’s Axe 5, headed by P. valduriez
(INRIA) and P. Larmande (IRD), was interested in several topics related to
scientific workflow (provenance, big data) as well as data integration
(ontology-based approaches). In this work-package, we have kicked-off the AgroPortal
(cf. above) and AgroLD platforms. The Agronomic
Linked Data knowledge base (AgroLD) mainly developed by P. Larmande (IRD), is
a knowledge system that exploits Semantic Web technology and relevant standard
domain ontologies, to integrate –genomics, proteomics and phenomics– information
on plant species widely studied by the agronomic research community. AgroLD is
a RDF knowledge base of 100M triples created by annotating and integrating more
than 50 datasets coming from 10 data sources with 10 ontologies. My
contributions within IBC were the leadership on AgroPortal project and
expertise in using ontologies for annotations in the AgroLD project.
Centre de Recherche et d'Innovation Industrielle (CR2i) DiagnosTIC-Santé project
The CR2I was an Investissement
d’Avenir French ANR program for industrial biomedical research. As member
of the metadata repository group (multi-omics platform development), we were interested
in offering a multi-omics data repository and defining standard vocabularies to
represent such data. Headed originally by Sanofi and Dr. Magali Roux, the
project led to the Kyomed spinoff (www.kyomed.com). My contribution within the CR2I
was knowledge engineering and modeling expertise.
National Center for Biomedical Ontology (NCBO)
NCBO (part of NIH National Centers for
Biomedical Computing Roadmap) is a consortium of leading biologists,
clinicians, informaticians, and ontologists who develop innovative technology
and services that allow scientists to create, disseminate, and manage
biomedical information and knowledge in machine-processable form. The project
vision is that all biomedical knowledge and data are disseminated on the
Internet using principled ontologies, such that the knowledge and data are
semantically interoperable and useful for furthering biomedical science and
clinical care. Important members of NCBO consortium are Stanford University,
Mayo Clinic, and University of Victoria. NCBO develops the BioPortal (http://bioportal.bioontology.org) platform. My contributions within
NCBO are detailed hereafter.
European Learning Grid Infrastructure (ELeGI)
The goal of the ELeGI project (www.elegi.org, IST Integrated Project EU – FP6)
was to promote a shift from the traditional e-learning approach
(content-centred) to an interaction based, collaborative and experimental one.
This new paradigm focused on knowledge construction using experimental based
and collaborative learning approaches in a contextualized, personalized and
ubiquitous way to replace the current information transfer paradigm focused on
content and on the key authoritative figure of the teacher who provides
information. The project aimed to propose a grid service-oriented architecture
to support this paradigm shift. Important members of ELeGI consortium were UM2,
Open University, Universities of Southampton, Dundee, Pau, St Andrews, ATOS
origin. Within the context of the ELeGI project we worked on a collaborative environment constructed over
a grid infrastructure called the Grid Shared Desktop (GSD). The GSD was a
Web-accessible environment that provides members of a virtual community with a
set of desktops supporting collaboration in both synchronous and asynchronous
mode. It is a powerful interface relying on grid service architecture to
communicate user representations and build collaborative knowledge. We
evaluated the GSD with a community of chemists tackling the problem of collaborative construction of an ontology
(using the ontology editor Protégé within the GSD). This work was done in
collaboration with Dr. M. Crubezy (Stanford Medical Informatics, USA), Dr.
C Laurenco (Institut Charles Gerhardt de Montpellier, France) and Pr. A. Krief
(Laboratoire de Chimie Organique Synthèse, Faculté N.-D de la Paix, Belgium).
Learning Grid of Excellence Working Group (LeGE-WG)
The project (IST STREP Project EU – FP6) aimed to facilitate the
establishment of a “European Learning Grid Infrastructure” by supporting the
systematic exchange of information and by creating opportunities for close
collaboration between the different actors in the formative process. The
project gave birth to the ELeGI project. My contribution within LeGE-WG took
the form of collaboration with Pr. Marc Eisenstadt (Knowledge Media Institute,
Open University, UK) and his group to propose a common vision based on learning
agents (artificial) and enhanced presence (human) for dynamic services.
As postdoctoral fellow at the Stanford
Center for Biomedical Informatics Research (BMIR), I was a member of Pr. M.
Musen's group. BMIR concentrates on the study of components for building
knowledge-based systems, controlled terminologies and ontologies, and
technology for the Semantic Web. For 30 years, this laboratory proposed
contributions to assist tasks in biomedicine. BMIR still develops Protégé the
most used ontology editor today. Within the National Center for Biomedical
Ontology (NCBO) project, we developed BioPortal consider today as the reference and most comprehensive Web repository for
biomedical ontologies and terminologies. This library contains a large
collection of ontologies in biomedicine in different format (OBO, OWL etc.)
such as Gene Ontology, NCI Thesaurus, ICD, FMA. Users can browse, search, and
comment ontologies both online and via a Web services API. The goal of NCBO was
to provide the biomedical community with a set of ontology-based services that
can be used by scientists to integrate their data and enhance translational discoveries (biomedical data integration problem).
In that context, I led conjunctly with Dr. Nigam H. Shah (PhD, MD) the semantic
annotation of biomedical data activities of the center. NCBO encourage
biomedical researchers to annotate their data with biomedical ontology concepts
for better data integration, search and discoveries. As main activity, I designed, implemented and experimented an
ontology-based annotation workflow to annotate text data with ontology
concepts. The workflow is based on syntactic concept recognition (using
concept names and synonyms) and on a set of semantic expansion algorithms that
leverage the semantics in ontologies (e.g., is_a relations, mappings, semantic
distance) to create new annotations. The annotation workflow relies on
BioPortal biomedical ontologies and generates annotations in several formats
like XML and RDF/OWL. We provide the
workflow as a web service: the NCBO Annotator (http://bioportal.bioontology.org/annotator) which is one of the most used
service of the platform today. Internally, we have used the annotation workflow
to index biomedical data resources with ontology concepts. The NCBO Resource Index (http://bioportal.bioontology.org/resources) allows a user to search for
biomedical data based on ontology concepts. The resource index is directly searchable
in the BioPortal ontology repository: when a user browses a given concept, he
has access (link) to the list of resource elements that have been annotated
with this concept. We have processed the textual metadata of elements from 20+
biomedical resources (e.g., abstract of articles (PubMed), gene expression data
sets (Array Express), clinical-trial reports (ClinicalTrials.gov)) and new ones
are still incorporated. We also use the annotation workflow to implement the NCBO Ontology Recommender service (http://bioportal.bioontology.org/recommender) which informs the user of the most
appropriate ontologies relevant for their given dataset using semantic
annotations. This service has been evaluated very useful by the community.
Developing the annotation workflow allows me to be interested in several
aspects related to ontologies and semantic web: (i) development and reuse
of semantic distances (graph/path based, or information content based),
(ii) development and management of ontology mappings, (iii) graph
algorithms (e.g., traverse, paths between concepts) to deal with the is_a
hierarchy structure, (iv) ontology and concept URIs to deal with ontology
versioning and annotations maintenance.
Software development
Within NCBO, I was involved in both research and development activities.
Being involved in all the stages of a development project from research to
prototype and to production is a very good learning experience of software
engineer practices (project management, code sharing, developer meetings,
technical questions, budget). Furthermore, the NCBO project was driven by
several “driving biological projects”. Being driven by those projects was very
interesting in terms of research, design and software development. It provided
direct feedback and evaluation that are instantly re-injected in the design
loop.
My thesis project was about dynamic
service exchange modelling. In a computing world where services become more
and more important, the project tackled the hard question: how services can be
dynamically and interactively constructed and exchanged in order to accurately
identify and fit the user problem. The notion of service is now at the centre
of distributed system development; it plays a key role in their implementation
and success. New needs in service exchange scenarios are clearly highlighted
(dynamicity, composition, conversation based, user-centred behaviour, customization,
business processes, semantics, etc.) by the service-oriented computing
community and are not addressed by current service oriented architectures
(e.g., web services). The next generation of services will consist of
dynamically generated services, i.e., services
constructed on the fly by the service provider according to the conversation it
has with the service user. In the thesis, I led a deep reflection about the
notion of service. I explain that providing a service means to identify and offer
a solution (among many possible ones) to the problem of another. A service is
not just a pre-determined product. I introduce the concept of dynamic
service generation as a different way to provide and use services in a
computer-mediated context: services are dynamically constructed, provided and
used by agents (human or artificial) within a community, by means of a
conversation. In dynamic service generation, the user agent is not assumed to
know exactly what the provider agent can offer him. He has to find out and
construct step by step what he wants based on the service provider’s reactions.
The central idea is that a service is based on a conversation. Actually,
dynamic service generation highlights the idea of processing something new
instead of merely delivering something that already exists such as in the
product approach. In everyday life, when somebody needs new clothes, buying ready-to-wear clothes is analogous to
asking for a product, whereas having
clothes made by a tailor is analogous to requiring a service to be
generated.
To address that big challenge we were interested in grid and multi-agent
systems. Grid because this is the first distributed architecture (and
infrastructure) really developed in a service-oriented perspective: grid
services are compliant web services, based on the dynamic allocation of
virtualized resources to an instantiated service. Grid services augment the
basic notion of web service with two significant features: service state and
service lifetime management. Whereas web services have instances that are
stateless and persistent, grid service instances can be either stateful or
stateless, and can be either transient or persistent. On the other hand, agents
are said to be autonomous, intelligent and interactive entities that may use
and provide services (in the sense of particular problem-solving capabilities).
Actually, agents have many interesting characteristics for service exchange:
they are reactive, efficient, adaptive, they know about themselves, they have a
memory and a persistent state, they are able to have conversation, work
collaboratively, negotiate, learn and reason to evolve, deal with semantics
associated to concepts by processing ontologies, etc. As they are based on a
conversation, a key indentified aspect to dynamically generate services was the
ability for services to have a state (grid) and then being able to
intelligently and dynamically modify this state (agent).
I made three precise contributions: (i) STROBE, a new agent
representation and communication model. STROBE is inspired by the three
Scheme primitives STReam, Object and Environment. STROBE agents are able to
interpret communication messages and execute services in a given dynamic
conversation context. These contexts are dedicated to a specific interlocutor
(or group of interlocutors). These contexts take the form of several
environments (with meta-programming techniques) in which agent capabilities and
messages are interpreted. Thanks to those environments an agent has a part of
its state that evolves according to the interactions it has with another agent.
A STROBE agent develops a dedicated language for each of its interlocutors.
This feature was exploited in the perspective of dynamic service generation. In
the context of service exchange, this feature allows an agent to dynamically
specify and execute a service. We illustrated such a scenario with a train
ticket booking service agent. Having dedicated and dynamic conversation context
is the key new aspect of the STROBE model. (ii) i-dialogue, a computational
abstraction that models multi-agents conversations by means of fundamental
constructs of applicative/functional languages (i.e., streams, lazy evaluation
and higher-order functions). An intertwined-dialogue
takes the form of a recursive function, producing and consuming streams of
messages, run by each agent in a multi-agents (more than two) conversation.
(iii) AGIL, a service-oriented
grid-agent integrated model based on the representation of agent
capabilities as grid services. Many works demonstrate the use of multi-agent
techniques for grid (e.g., agent based resource management) or merging web/grid
services standards with agents ones, but none of them propose a concrete
integration of the two paradigms. AGIL is a new, concrete and formalized
integration of the agent and grid paradigms. In this model, concepts of grid
and multi-agent systems, relations between them and the rules are semantically
described by a set-theory formalization and a common graphical description
language, called Agent-Grid Integration Language (AGIL) – also formalized as an ontology. AGIL aggregates the thesis results together by formalizing agent
interactions for service exchange on the grid. I demonstrate how such
integration is a great feature for services. For example, I demonstrate the
importance of the concept of state in service exchange (i.e., being able to
have a state, being able to dedicate a part of this state to an interlocutor
and being able to intelligently and dynamically modify this state). I highlight
how stateful and dynamic grid services (by opposition to stateless web
services) and agent dedicated conversation context are two complementary
approaches to deal with dynamic generated services. This integration model was
also inscribed in the perspective of dynamic service generation.
My thesis research project (3 years) was also done at LIRMM supervised
by Pr. Stefano A. Cerri. I had a French government MENRT fellowship. I wrote
and defended (November 16, 2006) my thesis in English. My defense jury included
3 thesis reviewers and was composed of some of the best international
scientists in these areas:
Michael N. Huhns, Pr.,
University of South Carolina, USA (rapporteur)
Luc Moreau, Pr., University of Southampton, UK (rapporteur)
Domenico Talia, Pr., Università della Calabria, Italy (rapporteur)
Amal El Fallah Seghrouchni Pr., Université Paris 6, France (examinateur)
Jacques Ferber, Pr., Université Montpellier II, France (examinateur)
Jean-Luc Koning, Pr., Inst. Nat. Polytechnique de Grenoble, France (examinateur)
Stefano A. Cerri, Pr., Université Montpellier II, France (directeur)
Software development
The development project done in the context of my PhD had a
proof-of-concept objective. The STROBE implementation project was done to
demonstrate with some experiments some important features of the STROBE model.
The two main experiments illustrate: (i) meta-level learning by communicating,
where STROBE agents modify their interpreters while communicating and learn a
new communicative acts by; ii) dynamic specification where STROBE agents
specify by interactions a function that must be executed to accomplish a
service (using non deterministic interpretation & constraints). I suggested
in this project to embed in an agent architecture a “reflexive tower” such as
the one available in functional/applicative languages (e.g., Scheme/LISP).
Using reflective programming techniques to dynamically change the way an
expression is evaluated is not an easy task. Doing it for agent architecture
was new. A first partial implementation was done in Scheme (to implement the
core of agent interpreters using reflective programming techniques). A second
one, StrobeKit, was done in Scheme/Java within the multi-agents platform MadKit and the Kawa framework to connect
Scheme and Java. The StrobeKit API enables a programmer to write agents that
respect STROBE model’s requirements concerning agent structure and agent
interaction. Details on STROBE implementation can be found Appendix C of my PhD
thesis.
We address the following problem: how can an agent change dynamically
(i.e., at run time) its behaviour based on messages it receives during a
conversation. We showed that using
meta-programming techniques (reflexivity/reification) in an agent architecture
an agent can actually dynamically modify the way it interprets messages and
then adapt its behaviour. For instance, in applicative/functional programming
languages, reflective programming allows an interpreter to be dynamically
(i.e., during the evaluation process) changed in order to access and eventually
modify the execution context (expression, environment,
interpreter, continuation) of a procedure. Embedded into agents, such a feature
enables them to dynamically learn at the data,
control and interpreter levels enabling them to change the way they interpret
messages in a conversation. We illustrate the model with an experiment where an
agent (as a Scheme interpreter) learn dynamically a new performative (speech
act for a message). This meta-level learning by communicating was envisaged as
a great feature to go toward the dynamic
service generation vision presented hereafter. This work lead to several
publications. Also, as MSc. student at UM2, I worked with some fellows on
different student “research” projects (usually a couple of months long): (i)
Warbot (robot agents) contest with the multi-agent
platform MadKit (advisor Pr. Jacques Ferber), (ii) coordination in cellular automata (advisor Dr. Philippe
Reitz).
My MSc research projects (6 months) was done at Laboratory of Informatics, Robotics, and Microelectronics of
Montpellier (LIRMM), University Montpellier 2 (UM2), within the Kayou team
concerned with topics such as agents and multi-agent systems, constraints,
machine learning, web, grid, service-oriented computing, ontologies,
collaborative learning. I was supervised by Pr. Stefano A. Cerri. Mainly, this
project initiated my PhD research project presented after. However, it allowed
me to get interested in some interesting tools for the future such as for
example applicative/functional programming languages (e.g., Scheme/Lisp).
(French) Details des activités d’enseignement
Mes activités d’enseignement sont en pause de 2015 à 2020 (5 années universitaires) pendant ma mobilité et la phase de retour de mon projet H2020 MSCA à l’Inria.
§ Depuis 2010 : Maitre de Conférences à l’École Polytechnique de Montpellier, composante de l’Université de Montpellier (192h~TD par an). De 2010 à 2015, j’étais responsable de 2 modules en 3ème et 5ème année d’école d’ingénieur et je participais à d’autres enseignements décris ci-après.
§ 2010-2015 : Je participai de manière investi et proactive à mon département d’enseignement en m’impliquant sur les activités périphériques du métier d’enseignant : recrutement des étudiants, salons, journées portes-ouvertes, maquettes, réunion pédagogiques, conseil de perfectionnement, etc.
§ 2010-2014 : Enseignements des modules de 5ème année IG à Polytech en anglais.
§ 2014 : Participation au 2ème Sommet du Numérique en Education, Montréal, Canada pour présenter nos travaux en innovation pédagogique à Polytech.
§ 2012 : J’ai produit une série complète de 8 conférences capturées en vidéos données aux étudiants de 5ème année de Polytech disponibles sur iTunesU: Cours Application Internet et Interopérabilité (AIOP).
§ 2006-2007 : ATER (complet) à l’Université Montpellier 3. Mon expérience d’enseignement (192h~TD) dans une université différente (arts, lettres, langues, sciences humaines et sociales) a été très enrichissante. Elle m’a permis d’intégrer une autre équipe d’enseignement et de côtoyer un autre public que celui de l’Université Montpellier 2 (sciences et techniques). J’y exerçais également des responsabilités communes et administratives.
§ 2003-2006 : Moniteur CIES à l’Université Montpellier 2. Le monitorat fut ma première expérience d’enseignement. En 3 ans (64h~TD/an), elle m’a permis d’exercer à petite échelle beaucoup des tâches de l’enseignant : préparation des cours/TD/TP, participation à l’évaluation (rédaction des sujets, corrections, jury), encadrement de projet et de stage, tâches administratives etc. J’ai aussi suivi un ensemble de formations (expression, théâtre, préparation, projets, etc.) proposées par le Centre d’Initiation à l’Enseignement Supérieur (CIES) de Montpellier.
§
Le
descriptif des cours que j’ai effectué est disponible à http://www.lirmm.fr/~jonquet/teaching
§ 2012-2015 : Responsable de la 5ème (et dernière) année de la filière « Informatique et Gestion ». Gestion de la maquette (2 options), des emplois du temps, et des intervenants extérieurs (~25 personnes).
§ 2012-2015 : Coordination de la cellule des enseignants de Polytech (70 personnes) qui s’intéressent à l’innovation pédagogique à l’aide des tablettes numériques (iPad). Nous avons décrit, testé et réalisé plusieurs scénarios d’utilisation des iPads dans la classe. Je m’occupais également d’une partie de la logistique du projet (1000 iPads). Voir : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01118757/document J’ai organisé également des formations chaque année avec un collaborateur d’Apple Éducation.
§ 2012-2015 : Correspondant Polytech pour le comité TICE (Technologies de l'information et de la communication pour l'éducation) de l’Université Montpellier 2. Nous avons organisé la conférence TICE 2014 à Béziers, France (~100 participants) et j’ai piloté l’organisation d’une session ReX (retour d’expérience) avec D. Cassagne.
§ 2015 (1 jour) : Formation UM ER10 « Gestion du temps et des priorités » par Jean-Yves L’Huillier (Vision Partagée).
§ 2015 (1/2 journée) : Formation UM ER02b « Comment organiser un enseignement dans le cadre d'une approche programme (de type Bologne/LMD) ».
§ 2015 (1/2 journée) : Conférence et suivi des formés UM ER02 : « Enseigner à l'université aujourd'hui : les grandes tendances de l'enseignement supérieur et leurs impacts sur les programmes d'enseignement » par Denis Berthiaume.
§ 2015 (2 jours) : Formation UM LA04 « Les techniques de réunion en anglais » par
§ 2014 (1,5 jour) : Formation UM/Polytech « Découverte de l'apprentissage actif» organisé par G. Cathébras.
§
2013,
2014, 2015 (3 jours) : Formation Polytech à l’utilisation de l’iPad pour
la pédagogie par Willy Dupont (formateur agrée Apple Éducation). Ces
formations (que je co-organisais) m’ont donné les outils et méthodes pour
introduire l’iPad dans mes cours. J’ai ensuite repris entièrement mon cours de
3ème année pour utiliser de manière active avec les édifiants les tablettes
pendant le cours grâce à des sondages, des exercices, des vidéos, etc.
L’expérience était très enrichissante et le retour valorisant (bien que pas
facile à mettre en place).
§ 2013
(3 jours) : Formation ER15 « Enrichir ses pratiques en pédagogie
universitaire » par Denis Berthiaume. Cette formation a été une
révélation aux techniques du métier d’enseignant. J’ai réellement compris les
tenants et aboutissants de la pratique grâce à cette formation (en 2 étapes).
§ 2013 (1/2 journée) : Formation ER19 « Utiliser la plateforme pédagogique Moodle » par DSI UM2.
§ 2013 (1 jour) : Formation ER35 « Créer des ressources multimédias pour l'enseignement ».
§ 2004-2006 (~7 jours) : Bouquet de formations à l’enseignement proposé aux Moniteurs CIES par l’IUFM de Montpellier. Dont une formation de 3 jours sur la voix et l’expression orale.
|
|
Enseignement |
Type |
Level |
Heures (~TD)/an |
|
(2013-2015) |
Web Sémantique |
CM |
Master |
6 |
|
(en 2011 seulement) |
Algorithmique et
programmation Ada/C |
TD/TP |
Licence |
40 |
|
Maitre de Conférences Polytech Montpellier (2010-2015) |
Architecture des
Ordinateurs |
CM |
Licence |
18 |
|
TD/TP |
Licence |
42 |
||
|
Applications Internet
et Interopérabilité |
CM |
Master |
18 |
|
|
TD/TP |
Master |
24 |
||
|
Encadrement stage |
- |
Master |
30 |
|
|
Encadrement PIFE |
- |
Master |
38 |
|
|
Divers cours |
|
Master |
4 |
|
|
Divers encadrement |
- |
Licence |
10 |
|
|
ATER Univ. Montpellier 3 (2006-2007) |
C2i niveau débutant |
CM/TD/TP |
Licence |
102 |
|
C2i niveau avancé |
CM/TD/TP |
Licence |
60 |
|
|
Internet/Php/Javascript |
CM/TD/TP |
Licence |
30 |
|
|
Moniteur CIES Univ. Montpellier 2 (2003-2006) |
Programmation/Scheme/évaluation |
TD |
Licence |
100 |
|
TP |
Licence |
40 |
||
|
Programmation/Algorith-mique/Maple |
TD |
Licence |
24 |
|
|
TP |
Licence |
20 |
||
|
Divers cours |
CM |
Licence |
9 |
|
|
Encadrement |
- |
Licence |
15 |
|
|
|
TOTAL : |
192*7 ans ~ 1400h
(~TD) |
||
§ 2013-2015 : Module « Web Sémantique »
Public : Ecole d’ingénieur « Informatique et Gestion », 5ème année.
Contribution : Cours inspiré de 2 tutoriaux (N. Noy & F. Gandon) et d’un listing d’applications du web sémantique. Gestion complète du module.
Objectifs : Le cours a pour objectif une introduction aux principes et technologies du web sémantique.
URL :
http://mon.univ-montp2.fr/claroline/course/index.php?cid=P1S904
§ 2010-2015 : Module « Applications Internet et Interopérabilité »
Public : Ecole d’ingénieur « Informatique et Gestion », 5ème année.
Contribution : Cours effectué en anglais (3 ans). ~300 transparents de cours. Gestion complète du module et des interventions extérieures sur J2EE et .NET.
Objectifs : Le cours a pour objectif la compréhension des architectures d'application Web. Une approche historique est suivie pour faire une revue des différents principes et modèles. Les technologies des applications Web et d'interopérabilité sont également présentées e.g., XML, J2EE, .NET, Web services, etc.
URL :
http://mon.univ-montp2.fr/claroline/course/index.php?cid=P1S911
§ 2010-2015 : Module « Architecture des Ordinateurs »
Public : Ecole d’ingénieur « Informatique et Gestion », 3ème année.
Objectifs : Le cours a pour objectif la compréhension de l’architecture des ordinateurs afin d’acquérir les connaissances de base utiles à la compréhension des autres disciplines de l’informatique. L’accent est notamment mis sur les principes de codage des données et des instructions et sur le fonctionnement de la mémoire et de l'unité centrale de traitement.
Contribution : ~240 transparents de cours et 3 feuilles de TD. Gestion complète du module.
URL : http://mon.univ-montp2.fr/claroline/course/index.php?cid=M513
§ 2011 : Module « Algorithmique et programmation »
Public : Ecole d’ingénieur « Informatique et Gestion », 3ème année.
Contribution : Intervention en TD/TP.
Objectifs : Compréhension des algorithmes comme une description précise et rigoureuse d’une suite d’opérations permettant d’obtenir, en un nombre fini d’étapes, la solution d’un problème. Type abstrait de données. Structure de données. La partie programmation aborde dans un premier temps le langage Ada puis le langage C.
URL :
http://mon.univ-montp2.fr/claroline/course/index.php?cid=PIG51P1S511
Responsable : Christophe Fiorio – fiorio@lirmm.fr
§ 2003&2004 : Module « Introduction à la programmation avec Scheme »
Public : 2ème année Deug MIAS (Mathématique, Informatique et Applications aux Sciences)
Objectifs : Ce module vise à introduire aux étudiants les concepts de base de l’abstraction procédurale, l’abstraction de données et des mécanismes d’évaluation (substitution, environnement, etc.) à l’aide d’un langage de programmation fonctionnel/applicatif, Scheme.
Contribution : Pour ce module, j’ai réalisé conjointement avec un collègue moniteur un ensemble de 8 nouvelles feuilles de TD et 6 nouvelles feuilles de TP ainsi que des encadrements de projets. Je me suis également occupé de l’organisation générale du module (équipe, réunions, réservation des salles, etc.).
Responsable : Stefano A. Cerri – cerri@lirmm.fr
n 2005 : Module « Introduction à l’algorithmique et à la programmation (Mapple) »
Public : 1ère année Licence (sciences)
Objectifs : Ce module vise à introduire aux étudiants les concepts de base de la programmation (variable, affectation, structure de contrôle, etc.) à l’aide d’un langage algorithmique puis d’un langage de programmation impérative, Maple.
Contribution : Module pour lequel j’ai intégré une équipe d’enseignement importante, ce qui m’a fait découvrir d’autres aspects de l’enseignement. Les feuilles de TD/TP existaient déjà.
Responsable : Philippe Janssen – janssen@lirmm.fr
URL :
http://ens.math.univ-montp2.fr/SPIP/ULIN101
n 2006 : « Certificat Informatique et Internet » (C2i niveau débutant et avancé))
Public : tous niveaux/toutes filières (lettres & sciences sociales)
Objectifs : Le C2i est un certificat national qui atteste de la compétence et de la maîtrise des technologies de l'information et de la communication. L’enseignement effectué n’est pas de l’Informatique « pure », mais de l’initiation à l’outil Informatique, à la bureautique et à Internet (forum, mails, HTML, etc.). Cela m’a permis de me confronter à des aspects plus pédagogiques que techniques de l’enseignement. Le public ayant très peu d’expérience en informatique.
Contribution : Participation à l’amélioration d’un cours existant. Contributions administratives et techniques.
Responsable : Patrice Séébold – seebold@lirmm.fr
URL : http://www.univ-montp3.fr/miap/ens/info/index.html
n
2007 :
Module « Informatique de
l’Internet »
Public : 2ème année, Licence MASS (Mathématiques Appliquées aux Sciences Sociales)
Objectifs : Module dont l’objectif est d’introduire aux étudiants les langages et les concepts de l’Internet (HTML, Java/Javascript, PHP, etc.).
Contribution : Mise à jour et reprise d’éléments de cours existants.
Responsable : Joël Quinqueton – jq@lirmm.fr
URL :
http://www.univ-montp3.fr/miap/ens/MASS/XLIN401/index.htm
Interventions diverses & Encadrements
§ 2020-2022 : Intervention dans le DU Scientific Data Management de l’Université de Montpellier.
§ 2019 : Intervention dans le module Web Sémantique du Master DECOL de la Faculté des Sciences de l’Université de Montpellier.
§ 2010-2015 : J’encadre également des stages de fin d’études (2 par an) et de projets industriels (2 par an). Participation à divers jurys.
§ 2010-2012 : Cours en Master TIC et Santé (UM2 et Institut Telecom).
§ 2006 : Cours en M2P Informatique de l’UM2 dans le module « Informatique Sociale ».
§ 2004 : Cours en DEA Informatique de l’UM2 dans le module « Système Multi-Agents ».