Clement Jonquet

PhD in Informatics
Associate Professor, University of Montpellier

Contact & Professional Situation

Born May 26, 1980, Nîmes (Gard), France, married, 2 children, French nationality.

University of Montpellier – LIRMM
161 rue Ada, 34095 Montpellier Cedex 5 – France

TEL: (+33/0) 467 41 97 43

 

SKYPE: clementpro – Email: jonquet@lirmm.fr – Twitter: @jonquet_lirmm
Web : www.lirmm.fr/~jonquet – ORCID: http://orcid.org/0000-0002-2404-1582
Public profiles: Google Scholar, Microsoft, ResearchGate, DBLP, HAL, PubMed, CiteSeer.

CV Strengths

§  Multidisciplinary research activities (Ontologies, Semantic Web, Ontology repositories, Biomedical Informatics, Semantic annotation, Text mining, Service-oriented computing, Web Science, Agents).

§  Experience in applied research (biomedicine, agronomy), software engineering & transfer skills.

§  Collaborative work experience, project funded research (EU, ANR, NIH), management skills (project leading, outsourcing, supervision).

§  Principal investigator of ANR JCJC (Young researcher program) SIFR project (2013-2017), Co-PI ANR PractiKPharma project (2016-2019), recipient of H2020 Marie Sklodowska-Curie grant (2016-2019), PI ANR D2KAB (2019-2023), Co-PI ANR FooSIN (2020-2022).

§  9 years of various academic teaching (~1400h ~TD) in Informatics/Computer Science to different student grades.

§  (Co)supervision of 12+ MSc. Students & 3 PhD, 6 postdocs, 3 engineers.

§  Mobility: 3-year postdoc and later 3-year visiting scholar at Stanford University.

Contents

Clement Jonquet 1

List of Publications 11

Detailed Resarch activity 20

(French) Details des activités d’enseignement 26

 

Work Experience

§  Since may 2019: Associate Professor (HDR), University of Montpellier, France.
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.

§  2010-2019: Assistant Professor, University of Montpellier, France.
Researcher in the Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (
LIRMM) and teacher at Polytech Montpellier Engineering School.

§  2007-2010: Postdoctoral scholar, Stanford University, USA
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’).

Education

§  2019: HDR in Informatics – University of Montpellier (French research direction habilitation)

§  2006: PhD in Informatics/Computer Science (First class with distinction) – UM2

§  2003: MSc in Computer Science (2.1 honours) – UM2 (~ French DEA & Maîtrise)

§  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)

Research Activity

Current Research Activity

I am interested in the convergence of French and English medical informatics ontology-based methods and tools in collaboration with Stanford BMIR. Especially in the use of ontologies and terminologies for knowledge extraction from text data e.g., French biomedical data or clinical notes. I develop and maintain an expertise on the BioPortal technology originally developed at Stanford with the vision to standardize ontology repositories and ontology-based services and promote data interoperability and FAIR ontologies. I am also interested in generalizing my work on semantic indexing and data annotation to other domain such as agronomy or biodiversity. I investigate new methods and knowledge engineering approaches in the context of designing a vocabulary and ontology repository for agronomy and related domains (AgroPortal project) as well as a semantic annotation workflow for French biomedical text data (SIFR project) used on real clinical data (PractiKPharma project). I lead the D2KAB project which focus on implementing methods to transform data into knowledge for agronomy and biodiversity. I am also interested in using ontologies for linked open data, knowledge graphs, automatic terminology extraction, text mining and natural language processing, ontology alignment, semantic similarity and graph-based approach for knowledge representation and collaborative learning. The Semantic Web in general.

Research Projects

§  2020-2022: Co-principal investigator of the FooSIN (French section of the GO FAIR Food Systems Implementation Network) – ANR head by S. Aubin, E DIPSO.

§  2019-2023: Principal investigator of the Data to Knowledge in Agronomy and Biodiversity (D2KAB) project ANR, 12-partner, 35-person project on semantics and linked data in agronomy & biodiversity.

§  2017-2019: VisaTM project. Text & Data mining infrastructure for French scientists. BSN-10 head by C. Nédellec, INRAE, Jouy-en-Josas.

§  2015-2023: Coordinator of the AgroPortal project, a vocabulary and ontology repository for agronomy, food, plant sciences and biodiversity, partially supported by ANR (SIFR, IBC, Labex NUMEV, Labex Agro, D2KAB) and EU-MSCA SIFRm.

§  2016-2019: Co-principal investigator of the PractriKPharma project (Practice-based evidences for actioning Knowledge in Pharmacogenomics) – ANR head by A. Coulet, INRIA, Nancy.

§  2013-2019: Principal investigator of the Semantic Indexing of French Biomedical Data Resources (SIFR) project – ANR Young Researcher & EU-MSCA. 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: Institut de Biologie Computationnelle (IBC), axe 5 (workflow & data integration) – ANR Inv. d’Avenir BioInfo. Development and use cases for AgroPortal & AgroLD.

§  2011-2013: 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).

§  2007-2010: National Center for Biomedical Ontology (NCBO) – Part of the National Centers for Biomedical Computing supported by the NIH Roadmap; provider of the NCBO BioPortal.

§  2003-2007: European Learning Grid Infrastructure (ELeGI) – IST IP EU (FP6).

§  2003-2004: Learning Grid of Excellence Working Group (LeGE-WG) – IST STREP EU (FP6).

Teams & Research Groups

§  2018-2020: Member, and co-head since 2019, of the LIRMM’s Fado team (Fuzziness, Alignments, Data & Ontologies).

§  2018-2010: 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 Musen’s lab and until 2017 of Dumontier’s lab at Stanford BMIR (medical informatics, knowledge representation and semantic Web (Protégé & BioPortal)).

§  2010-2018: Member of the LIRMM’s Smile team (multi-agent systems, Web science, service-oriented computing, ontologies, serious games, simulation).

§  2007-2010: Member of 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 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, Biomedical Informatics, Ontology alignment, Metadata, Linked Open Data, Knowledge representation, Data integration, Information Retrieval, Text mining, Service-oriented computing, Web Science, Distributed systems, Multi-Agents Systems, Web 2.0. Applications to biomedicine/health and agronomy/food/plant/biodiversity.

Grants (funding obtained as (co-)leader)

Since 2011, I have been independently supporting my research activities with different grants and funding sources; I obtained approximatively 2M€ of research funding over the last 10 years as summarized hereafter:

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-JS02-01001)

ANR JCJC call 2012

2013-2017

277K€

project

Stanford BMIR, CHU Rouen, UMR TETIS

Semantic indexing, ont-ology repositories, know-ledge 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 (701771)

H2020-MSCA-IF-2015

2016-2019

265K€

project

Stanford BMIR, INRIA (Zenith & Wimmics)

Support for mobility in the context of SIFR and 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 Versailles, CNRS-INIST

Text & data mining, semantic resources

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 International Research Laboratory

2019-2023

~14K€ (NA)

operating cost

LIRMM, Stanford (3 teams)

Medical robotics, underwater robotics and Semantic Web

#DigitAg internship fellowship

2020

7k€

intern

LIRMM, INRAE, ACTA

Encoding semantic resources for agriculture

FooSIN (ANR-19-DATA-0019)

ANR flash open science 2019 call

2020-2022

17K€

project

LIRMM, INRAE, IRD (+CIRAD)

French participation to GO FAIR Food Systems Implementation Network

Past Research Activity

§  NCBO project & postdoctoral research: Within NCBO I worked on semantic annotation of biomedical data with biomedical ontologies. I actively contributed to the NCBO BioPortal web application well used in the biomedical community. I designed an ontology-based annotation workflow. This workflow embeds different components (e.g., concept recognition tool, semantic expansion algorithms) in order to leverage the knowledge represented in ontologies and facilitate biomedical data integration. Based on this workflow, I conceptualized, designed, developed and experiment three research applications: (i) the NCBO Annotator, an ontology-based web service that can be used by the life sciences community to tag their data automatically with ontology concepts; (ii) the NCBO Resource Index, a database of open biomedical resources annotated and indexed with ontology concepts (20+ resources and 200+ ontologies at that time) which can be used to search and integrate data; (iii) the NCBO Recommender, a service which informs the user of the most appropriate ontologies relevant for their given dataset.

§  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 of 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.

Software Development & Technology

§  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/d2kab

§  2013-2018: Within the SIFR & AgroPortal projects:

o    Design of YAM-BIO a tool for ontology alignment with background knowledge resources (A. Annane’s PhD project).

o    Design, development & maintenance of the SIFR BioPortal (http://bioportal.lirmm.fr) (French medical terminologies) & AgroPortal (http://agroportal.lirmm.fr) projects.

o    Design & development of the SIFR/French Annotator and the NCBO Annotator+ both included within the SIFR BioPortal.

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.

§  BioPortal (http://bioportal.bioontology.org/), a web repository of biomedical ontologies developed by NCBO. I actively contributed to the evolution and design to the core NCBO BioPortal services and participate in the support to the community.

§  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.

Scientific Influence and dissemination

Seminars & Invited presentations

§  Over the last 12 years, I have been invited for 5 keynotes at conference, 4 project or lab seminars, 12 team or group seminars, and for 7 misc. meeting talks as described after.

§  Since 2016, I regularly organize tutorials on the use of ontology and ontology-based services with the platforms developed in my projects. I regularly teach to MSc. Students (e.g., U. Montpellier) and I have been invited to several summer schools or training events (5 in last 4 years) as described after.

§  I have 19 presentations on SlideShare cumulating ~11400 views.

Awards & Distinctions

§  2nd best poster award at the 14th Research Data Alliance plenary meeting (RDA P14), 2019.

§  Shared best paper award at 6th French Ontology Conference (JFO 2016).

§  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, 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 International Conference on Web Science (WebSci 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).

§  Semantic Web Challenge 2010 winner (with the NCBO team) at 9th International Semantic Web Conference (ISWC 2010) with the NCBO Resource Index.

Collaborations & Working groups

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 (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), INRA (P. Neveu, P. Buche), CNRS-CEFE (E. Garnier) on several use cases for AgroPortal. More recently in 2018, I have started a partnership with ANR network #DigitAg and IRSTEA (V. Bellon-Maurel) for data interoperability projects on digital agriculture.

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 INRA research groups (C. Pichot, C. Nédellec, C. Pommier) but also with INRA Scientific and Technical Information department (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 2019: New partners from D2KAB consortium: ACTA (F. Brun), IRSTEA (C. Roussey), CNRS I3S (C. Faron-Zucker, F. Michel).

§  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 (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/eRosa 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 2019: GO FAIR Food Systems Implementation Network.

§  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.

§  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.

§  Since 2016: AgBioData which gathers model organism databases in agriculture (mostly in the US).

§  Since 2016: Godan (Global Open Data for Agriculture and Nutrition) Action project and FAO (V. Pesce) on the Agrisemantics Map of Data Standards.

§  Since 2016: RDA Agrisemantics (S. Aubin, C. Caracciolo) working group with the IG on agriculture data.

§  Since 2015: RDA Wheat Data Interoperability working group (E. Dzalé), as a use case for AgroPortal.

Other ongoing collaborations:

§  Since 2019: LifeWatch ERIC (in ENVRI-FAIR H2020) in support on the development of EcoPortal.

§  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.

§  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 has allowed us to develop an expertise in Montpellier on ontology services and repositories.

Past collaborations:

§  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.

Profesionnal Responsabilities

Research or Working Group

§  2019-2020: Co-head of FADO research group at LIRMM with Pr. Anne Laurent. I am representing the team (6 permanents, 10-12 persons total) 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).

§  2012-2020: (Co)supervision of 12+ MSc. Students, 3 PhD, 6 postdocs, 3 engineers detailed after.

§  2010-2013: Organizer of the group of interest Web Science Montpellier Meetup (with a series of events).

Missions & Expertise

§  Project proposal reviewing and evaluation for French ANR (*3) and US NIH (*1).

§  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, 19 different international workhop or conference series & 8 national workshop or conference series. Detailled herafter.

Teaching & Other Responsibilities

§  2012-2015: Member of U. Montpellier 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

§  2020: Supervision & management of J. Lamarque (research engineer, D2KAB project).

§  2019-2020: Supervision of A. Laadhar and E. Amdouni (postdoc D2KAB project).

§  2019: Supervision of M. Mirzapour (postdoc PractiKPharma project).

§  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 project).

§  2016-2018: Co-supervision of A. Tchechmedjiev (postdoc PractiKPharma project) 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 project).

§  2015-2017: Supervision & management of V. Emonet (research engineer, SIFR project).

§  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 project).

§  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

§  Participation to the organization (with J. Azé) of 21émes Conférence d’Extraction et Gestion des Connaissances (EGC 2021), January 2011, Montpellier, France.

§  Steering committee for 3rd International Workshop on Semantics for Biodiversity (S4BIODIV 2020) at ISWC 2020.

§  Organization of the AgroHackathon series (in June 2016, July 2017, May 2020). ~15-30 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 International Workshop on Semantics for Biodiversity (S4BIODIV 2017) at ISWC 2017, Nov. 2017, Vienna, Austria. ~30 participants.

§  Participation to the organization (with S. Bringay) of 27émes Journées francophones d’Ingénierie des Connaissances (IC 2016), June 2016, Montpellier, France, ~100 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.

§  Local chair (with F. Scharffe) of 10th Extended Semantic Web Conference (ESWC 2013), May 26-30 2013, Montpellier, France. ~350 participants.

§  Co-program chair and organization committee of 1st International Workshop on Semantics for Biodiversity (S4BIODIV 2013) at ESWC 2013, May 2013, Montpellier, France. ~40 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

Data Intelligence (open access), Semantic Web Journal (IOS Press), Applied Ontology (IOS Press), Journal of Web Semantics (Elsevier), Bioinformatics (Oxford Journals), 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 Comittees

§  21st, 27th-28th Int. World Wide Web Conference (WWW 2018-2019, WWW 2012 (Demo track))

§  16th-17th Int. Semantic Web Conference (ISWC 2017-2018).

§  14th, 16th ,17th European Semantic Web Conference (ESWC 2017, 2019, 2020).

§  European Federation for Information Technology in Agriculture, Food & Environment (EFITA 2017).

§  1st Language, Data and Knowledge conference (LDK 2017)

§  1st-5th Int. Symposium on Information Management & Big Data (SIMBig 2014-2018).

§  11th-18th BioOntologies SIG (BioOntologies 2009-2017).

§  8th-11th Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2015-2016-2018).

§  11th &12th African Research in Computer Science and Applied Mathematics (CARI 2014-2016)

§  1st-2nd Int. Workshop on Semantics for Biodiversity (S4BIODIV 2013, 2017).

§  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 Comittees

§  24èmes-30èmes Journées francophones d’Ingénierie des Connaissances (IC 2013-2020).

§  1st & 2nd Atelier Web des données (AWD 2019, 2020).

§  Workshop Knowledge Engineering & Health (IA & Santé 2018 & 2019, SIIM 2015 & 2017, 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-3èmes 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).

Publication synthesis

Access & Citations

My complete list of publications is described below or in the HAL publication archive. I try to publish in open access journals (gold open access), but when not the case, a PDF is always available for every document (green open access) on HAL. Other incomplete listings include: Google Scholar, Microsoft Academic, ResearchGate, DBLP, PubMed, CiteSeer.

The first author is the “main” author. The last author is generally the supervisor. All publications (84) or communications (26) have been peer-reviewed (if not explicitly mentioned), including:

§  23 journal (6 as first author, 4 as second author, 3 as last author), 21 international conference, 15 workshop, 22 national (French) and 3 dissertations.

§  60 are international publications; most have been written in a collaborative context; more than 2/3 have been written by person(s) under my (co)supervision.

Overall my publications cumulate ~2650 citations as of Google Scholar (Feb. 2020); including 900 citations for publications as first author. Evolution of my citations (as of Google Scholar) is given aside.

Publication context and domains

§  Biomedical Informatics: 1 recent article in Journal of Biomedical Informatics (Elsevier, IF 3.23), 4 articles in BMC Bioinformatics (IF 3.45, CORE A) cumulating 280 citations, 1 in Nucleic Acids Research (Oxford, IF 10.16) with 855 citations, 2 application notes in Bioinformatics (Oxford, IF 7.31), 2 articles (one with 277 citations) at AMIA Symposiums which is one of the best venues to publish in this field. 2 articles (one with 93 citations) in BMC Biomedical Semantics (IF 2.41).

§  Semantic Web: 2 articles & 3 posters/demos (all cumulating 1!8 citations) in International Semantic Web Conference (CORE A), the main conference in the domain. Plus, the 1st prize at the 2010 Semantic Web Challenge and a corresponding publication (120 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 0.80) and in Knowledge Discovery in Bioinformatics (IGI Global) both cumulating 69 citations).

§  Agronomy & agriculture: multiple poster-demos and workshop papers recently published in this new field of application. One article as 1st author in Computers and Electronics in Agriculture (Elsevier, IF 2.5) with 34 citations. Two group articles in prestigious journals: Database (Oxford Academic, IF 3.98) and PLoS One (PLoS, 2.7). 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 0.65, CORE B) with 25 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. 9 French publications (over 20) are direct French versions of English papers; others are usually preliminary work.

Five Selected publications

§  [CJ2] 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. 6 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.

§  [CJ5] 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. 7 citations.

https://dx.doi.org/10.1007/s13740-018-0091-5

§  [CJ10] 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. 34 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 related to AgroPortal cumulates today 70 citations.

§   [CJ15] 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 International Semantic Web Conference, ISWC’10, Shanghai, China. 120 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 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 four publications on the topic cumulate 316 citations.

§   [CJ19] 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. 855 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.

§   [CJ41] 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. 277 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 512 citations.

Detailed Seminars & Invited presentations

Training & tutorial events

§  Lecture on ontology repository & ontology-based services, DECOL Master, U. Montpellier (invited by F. Ulliana), April 2019 & 2020.

§  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).

§  E-ENVIR CNRS thematic school, Gif-syr-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

§  AquaDiva BioGeo-Colloquium, Jena Univ., 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).

§  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, June 2003.

Summary of Teaching Activities

§  9 years of various academic teaching (~1400h ~TD) to different kind of students of mixed levels. Described in specific section.

§  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.

§  2012: One full series of 8 lectures given to Polytech students available on video on iTunesU: Internet Application and Interoperability (AIOP).

§  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.

Technical Skills

§  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 (RestLet).

§  Biomedical terminologies and ontologies (SNOMEDCT, MeSH, UMLS, OBO, etc.) as well as Semantic Web technologies (RDF/OWL/SKOS/SPARQL).

§  Database systems (SQL), good experience with 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).

Personnal topics

§  Experiences in several associations (student, sportive, social ones). 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.).

Languages

§  French: Mother tongue.

§  English: Very good (school & working knowledge), lived 6 years the USA.

§  Spanish: A few skills (from school).

§  Strong international orientation of work (publications & thesis manuscript written in English, international PhD defense jury and HDR jury, international postdoc).

Referees

§  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

List of Publications

Journal

[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]

23

International Conference

[24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]

21

Serie/Chapter

[45, 46, 47]

3

Workshop

[48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]

15

National (French) Conf.

[63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83]

22

Editor

[84, 85]

2

Dissertation

[86, 87, 88]

3

Poster & Demonstration

[89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116]

27

Reports

[117, 118, 119, 120, 121, 122, 123]

7

Journal

[1]    Pierre Monnin, Joe¨l Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clement Jonquet, Amedeo Napoli, and Adrien Coulet. PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC Bioinformatics, IN PRESS, 2019.

[2]    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, Dec.2018.

[3]    Aravind Venkatesan, Gildas Tagny, Nordine El Hassouni, Imene Chentli, Valentin Guignon, Clement Jonquet, Manuel Ruiz, and Pierre Larmande. Agronomic Linked Data: a knowledge system to enable integrative biology in Agronomy. PLoS One, 13(11):e0198270, November 2018.

[4]    Lisa Harper, Jacqueline Campbell, Ethalinda KS Cannon, Sook Jung, Dorrie Main, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Berardini, Clayton Birkett, Steve Cannon, James Carson, Bradford Condon, Laurel Cooper, Nathan Dunn, Chris Elsik, Andrew Farmer, Stephen Ficklin, David Grant, Emily Grau, Nic Herndon, Zhi-Liang Hu, Jodi Humann, Pankaj Jaiswal, Clement Jonquet, Marie-Ange´lique Laporte, Pierre Larmande, Gerard Lazo, Fiona McCarthy, Naama Menda, Christopher Mungall, Monica Munoz-Torres, Sushma Naithani, Rex Nelson, Daureen Nesdill, Carissa Park, James Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak Unni, Liya Wang, Doreen Ware, Jill Wegrzyn, Jason Williams, and Margaret Woodhouse. AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture. Database, page bay088, September 2018.

[5]    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.

[6]    Amina Annane, Zohra Bellahsene, Faic¸cal Azouaou, and Clement Jonquet. Building an effective and efficient background knowledge resource to enhance ontology matching. Web Semantics, 51:51–68, August 2018.

[7]    Juan Antonio Lossio-Ventura, Jiang Bian, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. A novel framework for biomedical entity sense induction. Biomedical Informatics, 84:31–41, August 2018.

[8]    Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Soumia Melzi, Jitendra Jonnagaddala, and Clement Jonquet. Enhanced Functionalities for Annotating and Indexing Clinical Text with the NCBO Annotator+. Bioinformatics, page 3, January 2018.

[9]    Esther Dzale-Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Robert P. Davey, Richard A. Fulss, Clement Jonquet, Marie-Ange´lique Laporte, Pierre Larmande, Cyril Pommier, Vassilis Protonotarios, Carmen Reverte, Rosemary Shrestha, Imma Subirats, Aravind Venkatesan, Alex Whan, and Hadi Quesneville. Developing data interoperability through standards: a wheat community use case. F1000 Research, 6(1843), December 2017.

[10] Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzale-Yeumo, Vincent Emonet, John Graybeal, Marie-Ange´lique Laporte, Mark A. Musen, Valeria Pesce, and Pierre Larmande. AgroPortal: a vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture, 144:126–143, January 2018.

[11] Philippe Lemoisson, Guillaume Surroca, Clement Jonquet, and Stefano A. Cerri. ViewpointS: capturing formal data and informal contributions into an adaptive knowledge graph. Knowledge and Learning, 12(2):119–145, May 2018.

[12] Marcos Martinez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos, and Mark A. Musen. NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation. Biomedical Semantics, 8(21), June 2017.

[13] Juan-Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Biomedical term extraction: overview and a new methodology. Information Retrieval, Special issue on Medical Information Retrieval, 19(1):59–99, August 2015.

[14] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Towards a mixed approach to extract biomedical terms from text corpus. Knowledge Discovery in Bioinformatics, 4(1):15, 2014.

[15] 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 International Semantic Web Conference, ISWC’10, Shanghai, China.

[16] Christophe Roeder, Clement Jonquet, Nigam H. Shah, William A. Baumgartner Jr, and Lawrence Hunter. A UIMA Wrapper for the NCBO Annotator. Bioinformatics, 26(14):1800–1801, May 2010.

[17] Clement Jonquet, Mark A. Musen, and Nigam H. Shah. Building a Biomedical Ontology Recommender Web Service. Biomedical Semantics, 1(S1), June 2010. Selected in Pr. R. Altman’s 2011 Year in Review at AMIA TBI.

[18] Nigam H. Shah, Nipun Bhatia, Clement Jonquet, Daniel L. Rubin, Annie P. Chiang, and Mark A. Musen. Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinformatics, 10(9:S14), September 2009.

[19] 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.

[20] Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, and Mark A. Musen. Ontology-driven Indexing of Public Datasets for Translational Bioinformatics. BMC Bioinformatics, 10(2:S1), February 2009.

[21] Clement Jonquet, Pascal Dugenie, and Stefano A. Cerri. Agent-Grid Integration Language. Multiagent and Grid Systems, 4(2):167–211, 2008.

[22] Pascal Duge´nie, Philippe Lemoisson, Clement Jonquet, and Monica Crube´zy. The Grid Shared Desktop: a bootstrapping environment for collaboration. Advanced Technology for Learning, Special issue on Collaborative Learning, 3(4):241–249, 2006.

[23] Clement Jonquet and Stefano A. Cerri. The STROBE model: Dynamic Service Generation on the Grid. Applied Artificial Intelligence, Special issue on Learning Grid Services, 19(9-10):967–1013, October-November 2005.

International Conference

[24] Biswanath Dutta, Anne Toulet, Vincent Emonet, and Clement Jonquet. New Generation Metadata vocabulary for Ontology Description and Publication. In E. Garoufallou, S. Virkus, R. Siatri, and D. Koutsomiha, editors, 11th Metadata and Semantics Research Conference, MTSR’17, volume 755 of Communications in Computer and Information Science, pages 173–185, Tallinn, Estonia, November 2017. Springer.

[25] Philippe Lemoisson, Guillaume Surroca, Clement Jonquet, and Stefano A. Cerri. ViewpointS: When Social Ranking Meets the Semantic Web. In V. Rus and Z. Markov, editors, 30th International Florida Artificial Intelligence Research Society Conference, FLAIRS’17, pages 329–334, Marco Island, FL, USA, May 2017. AAAI Press.

[26] Sole`ne Eholie´, Mike-Donald Tapi-Nzali, Sandra Bringay, and Clement Jonquet. MuEVo, a breast cancer Consumer Health Vocabulary built out of web forums. In A. Paschke, A. Burger, A. Splendiani, M.S. Marshall, and P. Romano, editors, 9th International Semantic Web Applications and Tools for Life Sciences, SWAT4LS’16, page 10, Amsterdam, The Netherlands, December 2016.

[27] Amina Annane, Zohra Bellahsene, Faical Azouaou, and Clement Jonquet. Selection and Combination of Heterogeneous BK to Enhance Biomedical Ontology Matching. In E. Blomqvist, P. Ciancarini, F. Poggi, and F. Vitali, editors, 20th International Conference on Knowledge Engineering and Knowledge Management, EKAW’16, volume 10024 of Lecture Notes in Artificial Intelligence, pages 19–33, Bologna, Italy, November 2016. Springer.

[28] Guillaume Surroca, Philippe Lemoisson, Clement Jonquet, and Stefano A. Cerri. Subjective and generic distance in ViewpointS: an experiment on WordNet. In 6th International Conference on Web Intelligence, Mining and Semantics, WIMS’16, number 11, page 6, Nimes, France, June 2016. ACM.

[29] Amina Annane, Vincent Emonet, Faical Azouaou, and Clement Jonquet. Multilingual Mapping Reconciliation between English-French Biomedical Ontologies. In 6th International Conference on Web Intelligence, Mining and Semantics, WIMS’16, number 13, page 12, Nimes, France, June 2016. ACM.

[30] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Automatic Biomedical Term Polysemy Detection. In 10th International Conference on Language Resources and Evaluation, LREC’16, pages 23–28, Portoroz, Slovenia, May 2016. European Language Resources Association.

[31] Guillaume Surroca, Philippe Lemoisson, Clement Jonquet, and Stefano A. Cerri. Preference Dissemination by Sharing Viewpoints: Simulating Serendipity. In 7th Intertnational Conference on Knowledge Engineering and Ontology Development KEOD’15, volume 2, pages 402–409, Lisbon, Portugal, November 2015.

[32] Soumia Melzi and Clement Jonquet. Scoring semantic annotations returned by the NCBO Annotator. In A. Paschke, A. Burger, P. Romano, M.S. Marshall, and A. Splendiani, editors, 7th International Semantic Web Applications and Tools for Life Sciences, SWAT4LS’14, volume 1320 of CEUR Workshop Proceedings, page 15, Berlin, Germany, December 2014. CEUR-WS.org.

[33] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Yet Another Ranking Function for Automatic Multi-word Term Extraction. In A. Przepiorkowski and M. Ogrodniczuk, editors, 9th International Conference on Natural Language Processing, PolTAL’14, volume 8686 of Lecture Notes in Artificial Intelligence, pages 52–64, Warsaw, Poland, September 2014. Springer.

[34] Julien Grosjean, Lina F. Soualmia, Khedidja Bouarech, Clement Jonquet, and Stefan J. Darmoni. An Approach to Compare Bio-Ontologies Portals. In C. Lovis, B. Se´roussi, A. Hasman, L. Pape-Haugaard, O. Saka, and S.K. Andersen, editors, 26th International Conference of the European Federation for Medical Informatics, MIE’14, volume 205 of Studies in Health Technology and Informatics, pages 1008–1012, Istanbul, Turkey, September 2014. IOS Press.

[35] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Integration of Linguistic and Web Information to Improve Biomedical Terminology Extraction. In A-M. Almeida, J. Bernardino, and E. F. Gomes, editors, 18th International Database Engineering & Applications Symposium, IDEAS’14, pages 265–269, Porto, Portugal, July 2014. ACM.

[36] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Combining C-value and Keyword Extraction Methods for Biomedical Terms Extraction. In 5th International Symposium on Languages in Biology and Medicine, LBM’13, pages 45–49, Tokyo, Japan, December 2013. Database Center for Life Science.

[37] Clement Jonquet, Paea LePendu, Sean M. Falconer, Adrien Coulet, Natalya F. Noy, Mark A. Musen, and Nigam H. Shah. NCBO Resource Index: OntologyBased Search and Mining of Biomedical Resources. In C. Bizer and D. Maynard, editors, Semantic Web Challenge, 9th International Semantic Web Conference, ISWC’10, page 8, Shanghai, China, November 2010. 1st prize.

[38] Paea LePendu, Natalya F. Noy, Clement Jonquet, Paul R. Alexander, Nigam H. Shah, and Mark A. Musen. Optimize First, Buy Later: Analyzing Metrics to Ramp-up Very Large Knowledge Bases. In P. F. Patel-Schneider, Y. Pan, P. Hitzler, P. Mika, L. Zhang, J. Z. Pan, I. Horrocks, and B. Glimm, editors, 9th International Semantic Web Conference, ISWC’10, volume 6496 of Lecture Notes in Computer Science, pages 486–501, Shanghai, China, November 2010. Springer.

[39] Gautam K. Parai, Clement Jonquet, Rong Xu, Mark A. Musen, and Nigam H. Shah. The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. In American Medical Informatics Association Annual Symposium, AMIA’10, Washington, DC, USA, November 2010.

[40] Amir Ghazvinian, Natasha F. Noy, Clement Jonquet, Nigam H. Shah, and Mark A. Musen. What Four Million Mappings Can Tell You about Two Hundred Ontologies. In A. Bernstein, D. R. Karger, T. Heath, L. Feigenbaum, D. Maynard, E. Motta, and K. Thirunarayan, editors, 8th International Semantic Web Conference, ISWC’09, volume 5823 of Lecture Notes in Computer Science, pages 229–242, Washington DC, USA, November 2009. Springer.

[41] 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.

[42]  Clement Jonquet, Mark A. Musen, and Nigam H. Shah. A System for Ontology-Based Annotation of Biomedical Data. In A. Bairoch, S. Cohen-Boulakia, and C. Froidevaux, editors, International Workshop on Data Integration in the Life Sciences, DILS’08, volume 5109 of Lecture Notes in BioInformatics, pages 144– 152, Evry, France, June 2008. Springer.

[43] Stefano A. Cerri, Monica Crube´zy, Pascal Duge´nie, Clement Jonquet, and Phillippe Lemoisson. The Grid Shared Desktop for CSCL. In P. Cunningham and M. Cunningham, editors, eChallenges 2006 Conference, volume 3 of Information and Communication Technologies and the Knowledge Economy, pages 1493–1499, Barcelona, Spain, October 2006. IOS Press.

[44] Clement Jonquet and Stefano A. Cerri. i-dialogue: modeling agent conversation by streams and lazy evaluation. In International Lisp Conference, ILC’05, pages 219–228, Stanford University, CA, USA, June 2005.

Series/Chapter

[45] Clement Jonquet Pascal Neveu, Romain David. Improving Data Management and Decision Support Systems in Agriculture, volume 85 of Series in Agricultural Science, chapter Improving data identification and tagging for more effective decision making in agriculture. Burleigh Dodds Science Publishing, Cambridge, UK, March 2020.

[46] Clement Jonquet. Semantic Indexing of French Biomedical Data Resources. Project Repository Journal, 3:16–19, November 2019. Not reviewed dissemination ar- ticle.

[47] Clement Jonquet, Marc Eisenstadt, and Stefano A. Cerri. Learning agents and Enhanced Presence for generation of services on the Grid. In P. Ritrovato, C. Al- lison, S.A. Cerri, T. Dimitrakos, M. Gaeta, and S. Salerno, editors, Towards the Learning GRID: advances in Human Learning Services, volume 127 of Frontiers in Artificial Intelligence and Applications, pages 203–213. IOS Press, November 2005.

Workshop

[48] Andon Tchechmedjiev and Clement Jonquet. Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation. In Workshop on Language, Ontology, Terminology and Knowledge Structures, LOTKS’17, number W17-7007, page 8, Montpellier, France, September 2017. ACL.

[49] Clement Jonquet. Challenges for ontology repositories and applications to biomedicine & agronomy. In J.L. Lossio-Ventura and H. Alatrista-Salas, editors, 4th Annual International Symposium on Information Management and Big Data, SIMBig’17, volume 2029 of CEUR Workshop Proceedings, pages 25–37, Lima, Peru, September 2017. Keynote Speaker Paper.

[50] Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, and Clement Jonquet. ICD10 Coding of Death Certificates with the NCBO and SIFR Annotator(s) at CLEF eHealth 2017 Task 1. In Working Notes of CLEF eHealth Evaluation Lab, volume 1866 of CEUR Workshop Proceedings, page 16, Dublin, Ireland, September 2017.

[51] Pierre Monnin, Clement Jonquet, Joel Legrand, Amedeo Napoli, and Adrien Coulet. PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. In Network Tools and Applications in Biology Workshop, NETTAB’17, Preprints, page 4, Palermo, Italy, October 2017. PeerJ. Peer reviewed by NETTAB’17 PC.

[52] Clement Jonquet, Anne Toulet, and Vincent Emonet. Two years after: a review of vocabularies and ontologies in AgroPortal. In International Workshop on sources and data integration in agriculture, food and environment using ontologies, IN-OVIVE’17, page 13, Montpellier, France, July 2017. EFITA.

[53] Clement Jonquet, Vincent Emonet, and Mark A. Musen. Roadmap for a multilingual BioPortal. In J. Gracia, J.P. McCrae, and G. Vulcu, editors, 4th Workshop on the Multilingual Semantic Web, MSW4’15, volume 1532 of CEUR Workshop Proceedings, pages 15–26, Portoroz, Slovenia, June 2015.

[54] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. SIFR project: The Semantic Indexing of French Biomedical Data Resources. In J.A. Lossio-Ventura and H. Alatrista-Salas, editors, 1st International Symposium on Information Management and Big Data, SIMBig’14, volume 1318 of CEUR Workshop Proceedings, pages 58–61, Cusco, Peru, September 2014.

[55] Julien Grosjean, Lina F. Soualmia, Khedidja Bouarech, Clement Jonquet, and Stefan J. Darmoni. Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal? In 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO’14, page 11, Granada, Spain, April 2014.

[56] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Biomedical Terminology Extraction: A new combination of Statistical and Web Mining Approaches. In E. Nee, J-M. Daube, M. Valette, and S. Fleury, editors, 12th International Workshop on Statistical Analysis of Textual Data, JADT’14, pages 421–432, Paris, France, June 2014.

[57] Clement Jonquet, Nigam H. Shah, and Mark A. Musen. Prototyping a Biomedical Ontology Recommender Service. In Bio-Ontologies: Knowledge in Biology, SIG, ISMB-ECCB’09, pages 65–68, Stockholm, Sweden, July 2009.

[58] Pascal Duge´nie, Clement Jonquet, and Stefano A. Cerri. The Principle of Immanence in GRID-Multiagent Integrated Systems. In R. Meersman, Z. Tari, and P. Herrero, editors, 4th International Workshop On Agents and Web Services Merging in Distributed Environments, AWeSOMe’08, OTM 2008 Workshops, volume 5333 of Lecture Notes in Computer Science, pages 98–107, Monterrey, Mexico, November 2008. Springer.

[59] Clement Jonquet, Pascal Dugenie, and Stefano A. Cerri. Service-Based Integration of Grid and Multi-Agent Systems Models. In R. Kowalczyk, M.N. Huhns, M. Klusch, Z. Maamar, and Q.B. Vo, editors, International Workshop on Service-Oriented Computing: Agents, Semantics, and Engineering, SOCASE’08, volume 5006 of Lecture Notes in Computer Science, pages 56–68, Estoril, Portugal, May 2008. Springer.

[60] Fre´de´ric Duvert, Clement Jonquet, Pascal Duge´nie, and Stefano A. Cerri. AgentGrid Integration Ontology. In R. Meersman, Z. Tari, and P. Herrero, editors, 2nd International Workshop on Agents, Web Services and Ontologies Merging, AWeSOMe’06, volume 4277 of Lecture Notes in Computer Science, pages 136– 146, Montpellier, France, November 2006. Springer.

[61] Clement Jonquet and Stefano A. Cerri. Agents Communicating for Dynamic Service Generation. In 1st International Workshop on Grid Learning Services, GLS’04, pages 39–53, Maceio, Brazil, September 2004.

[62] Stefano A. Cerri, Marc Eisenstadt, and Clement Jonquet. Dynamic Learning Agents and Enhanced Presence on the Grid. In 3rd International LeGE-WG Workshop: Grid Infrastructure to Support Future Technology Enhanced Learning, Berlin, Germany, December 2003. Electronic Workshops in Computing.

National (French) Conference

[63] Sophie Aubin, Pierre Bisquert, Patrice Buche, Juliette Dibie, Liliana Ibanescu, Clement Jonquet, and Catherine Roussey. Recent progresses in data and knowl- edge integration for decision support in agri-food chains. In N. Hernandez, editor, 30e`mes Journe´es Francophones d’Inge´nierie des Connaissances, IC’19, pages 43–59, Toulouse, France, July 2019.

[64] Clement Jonquet. Maitriser une technologie de gestion des ontologies et vocabulaires en France : de´fis et enjeux. In SemWebPro Conference, page 2, Paris, France, November 2018.

[65] Fabienne Kettani, Ste´phane Schneider, Sophie Aubin, Robert Bossy, Claire Franc¸ois, Clement Jonquet, Andon Tchechmedjiev, Anne Toulet, and Claire Ne´dellec. Projet VisaTM : l’interconnexion OpenMinTeD AgroPortal ISTEX, un exemple de service de Text et Data Mining pour les scientifiques franc¸ais. In Sylvie Rawnez, editor, 29e`mes Journe´es Francophones d’Inge´nierie des Connaissances, IC’18, Poster Session, pages 247–249, Nancy, France, July 2018.

[66] Amine Abdaoui, Andon Tchechmedjiev, William Digan, Sandra Bringay, and Clement Jonquet. French ConText: De´tecter la ne´gation, la temporalite´ et le sujet dans les textes cliniques Franc¸ais. In 4e`me Symposium sur l’Inge´nierie de l’Information Me´dicale, SIIM’17, page 10, Toulouse, France, November 2017.

[67] Anne Toulet, Vincent Emonet, and Clement Jonquet. Mode`le de me´tadonne´es dans un portail d’ontologies. In G. Diallo and O. Kazar, editors, 6e`mes Journe´es Francophones sur les Ontologies, JFO’16, Bordeaux, France, October 2016. Best paper award.

[68] Clement Jonquet, Amina Annane, Khedidja Bouarech, Vincent Emonet, and Soumia Melzi. SIFR BioPortal : Un portail ouvert et ge´ne´rique d’ontologies et de terminologies biome´dicales franc¸aises au service de l’annotation se´mantique. In 16th Journe´es Francophones d’Informatique Me´dicale, JFIM’16, page 16, Gene`ve, Suisse, July 2016.

[69] Sole`ne Eholie´, Mike Donald Tapi Nzali, Sandra Bringay, and Clement Jonquet. MuEVo, un vocabulaire multi-expertise (patient/me´decin) de´die´ au cancer du sein. In 2e`me Atelier sur l’Intelligence Artificielle et la Sante´, page 7, Montpellier, France, June 2016.

[70] Amina Annane, Vincent Emonet, Faical Azouaou, and Clement Jonquet. Re´conciliation d’alignements multilingues dans BioPortal. In Nathalie Pernelle, editor, 27e`mes Journe´es Francophones d’Inge´nierie des Connaissances, IC’16, number 18, page 12, Montpellier, France, June 2016.

[71] Clement Jonquet, Esther Dzale´-Yeumo, Elizabeth Arnaud, and Pierre Larmande. AgroPortal: a proposition for ontology-based services in the agronomic domain. In 3e`me atelier INte´gration de sources/masses de donne´es he´te´roge`nes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement, IN-OVIVE’15, page 5, Rennes, France, June 2015.

[72] Guillaume Surroca, Philippe Lemoisson, Clement Jonquet, and Stefano A. Cerri. Diffusion de syste`mes de pre´fe´rences par confrontation de points de vue, vers une simulation de la Se´rendipite´. In 26e`mes Journe´es Francophones d’Inge´nierie des Connaissances, IC’15, page 12, Rennes, France, June 2015.

[73] Juan-Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Pre´diction de la polyse´mie pour un terme biome´dical. In E. Gaussier, editor, 12e`me COnfe´rence en Recherche d’Information et Applications, CORIA’15, pages 437–452, March, Paris, France 2015.

[74] Clement Jonquet and Mark A. Musen. Gestion du multilinguisme dans un portail d’ontologies : e´tude de cas pour le NCBO BioPortal. In C. Roche, R. Costa, and E. Coudyzer, editors, Terminology & Ontology : Theories and applications Workshop, TOTh’14, page 2, Brussels, Belgium, December 2014.

[75] Clement Jonquet, Christophe Fiorio, Philippe Papet, Ste´phanie Belin-Mejean, Claudine Pastor, and ’Cellule iPad des enseignants de Polytech Montpellier’. REX : Innovation pe´dagogique via l’utilisation de tablettes nume´riques a` Polytech Montpellier. In D. Casssagne and C. Jonquet, editors, 9e`me confe´rence des Technologies de l’Information et de la Communication pour l’Enseignement, TICE’14, Session Retour d’Expe´rience (REX), pages 97–106, Be´ziers, France, November 2014.

[76] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. Extraction automatique de termes combinant diffe´rentes informations. In Brigitte Bigi, editor, 21e`me Traitement Automatique des Langues Naturelles, TALN’14, volume 2, pages 407–412, Marseille, France, July 2014.

[77] Guillaume Surroca, Philippe Lemoisson, Clement Jonquet, and Stefano A. Cerri. Construction et e´volution de connaissances par confrontation de points de vue : prototype pour la recherche d’information scientifique. In Catherine FaronZucker Catherine Roussey, editor, 25e`mes Journe´es Francophones d’Inge´nierie des Connaissances, IC’14, page 12, Clermont-Ferrand, France, Mai 2014.

[78] Clement Jonquet, Adrien Coulet, Nigam H. Shah, and Mark A. Musen. Indexation et inte´gration de ressources textuelles a` l’aide d’ontologies : application au domaine biome´dical. In S. Despres, editor, 21e`mes Journe´es Francophones d’Inge´nierie des Connaissances, IC’10, pages 271–282, Nimes, France, June 2010.

[79] Clement Jonquet, Nigam H. Shah, and Mark A. Musen. Un service Web pour l’annotation se´mantique de donne´es biome´dicales avec des ontologies. In M. Fieschi, P. Staccini, O. Bouhaddou, and C. Lovis, editors, 13e`mes Journe´es Francophones d’Informatique Me´dicale, JFIM’09, volume 17 of Informatique et Sante´, Nice, France, April 2009.

[80] Clement Jonquet, Pascal Duge´nie, and Stefano A. Cerri. Inte´gration oriente´e service des mode`les Grid et Multi-Agents. In V. Chevrier and M-P. Huget, editors, 14e`mes Journe´es Francophones sur les Syste`mes Multi-Agents, JFSMA’06, pages 271–274, Annecy, France, October 2006. Herme`s.

[81] Clement Jonquet and Stefano A. Cerri. Agents as Scheme Interpreters: Enabling Dynamic Specification by Communicating. In 14th Congre`s Francophone AFRIF-AFIA de Reconnaissance des Formes et Intelligence Artificielle, RFIA’04, volume 2, pages 779–788, Toulouse, France, January 2004.

[82] Clement Jonquet and Stefano A. Cerri. Apprentissage issu de la communication pour des agents cognitifs. In J-P. Briot and K. Ghe´dira, editors, 11e`mes Journe´es Francophones sur les Syste`mes Multi-Agents, JFSMA’03, pages 83– 87, Hammamet, Tunisia, November 2003. Herme`s.

[83] Clement Jonquet and Stefano A. Cerri. Cognitive Agents Learning by Communicating. In Colloque Agents Logiciels, Coope´ration, Apprentissage et Activite´ Humaine, ALCAA’03, pages 29–39, Bayonne, France, September 2003.

Editor

[84] Alsayed Algergawy, Naouel Karam, Friederike Klan, and Clement Jonquet, editors. Proceedings of the 2nd International Workshop on Semantics for Biodiversity, S4BioDiv’17, volume 1933 of CEUR Workshop Proceedings, Vienna, Austria, October 2017.

[85] Pierre Larmande, Elizabeth Arnaud, Isabelle Mougenot, Clement Jonquet, The´re`se Libourel, and Manuel Ruiz, editors. Proceedings of the 1st International Workshop on Semantics for Biodiversity, S4BioDiv’13, Montpellier, France, May 2013.

Dissertation

[86] Clement Jonquet. Ontology Repository and Ontology-Based Services – Challenges, contributions and applications to biomedicine & agronomy. HDR manuscript, University of Montpellier, Montpellier, France, May 2019.

[87] Clement Jonquet. Dynamic Service Generation: Agent interactions for service exchange on the Grid. PhD thesis, University Montpellier 2, Montpellier, France, November 2006.

[88] Clement Jonquet. Communication agent et interpre´tation Scheme pour l’apprentissage au me´ta-niveau. Master thesis, University Montpellier 2, Montpellier, France, June 2003.

Poster & Demonstration

[89] Sophie Aubin, Anne-Franc¸oise Adam-Blondon, Michael Alaux, Mouhamadou Ba, Stephan Bernard, Pierre Bisquert, Robert Bossy, Franc¸ois Brun, Patrice Buche, Arnaud Castelltort, Olivier Corby, Julien Cufi, Romain David, Louise Dele´ger, Esther Dzale´-Yeumo, Catherine Faron Zucker, Eric Garnier, John Graybeal, The´o-Paul Haezebrouck, Pierre Larmande, Luc Menut, Franck Michel, Mark Musen, Claire Ne´dellec, Christian Pichot, Franc¸ois Pinet, Cyril Pommier, Catherine Roumet, Catherine Roussey, Konstantin Todorov, Anne Toulet, and Clement Jonquet. D2KAB project taking off: Data to Knowledge in Agronomy and Biodiversity. In 14th Plenary Meeting of the Research Data Al- liance, Poster session, Helsinki, Finland, October 2019. 2nd best poster award.

[90] John Graybeal, Clement Jonquet, Nicola Fiore, and Mark A. Musen. Adoption of BioPortal’s Ontology Registry Software: The Emerging OntoPortal Commu- nity. In 13th Plenary Meeting of the Research Data Alliance, Poster session, Philadelphia, PA, USA, April 2019.

[91] Nordine El Hassouni, Manuel Ruiz, Anne Toulet, Clement Jonquet, and Pierre Larmande. The Agronomic Linked Data (AgroLD) project. In European conference dedicated to the future use of ICT in the agri-food sector, bioresource and biomass sector, EFITA’17, demonstration session, page 257, Montpellier, France, July 2017.

[92] Clement Jonquet, Anne Toulet, Vincent Emonet, and Pierre Larmande. AgroPortal: an ontology repository for agronomy. In European conference dedicated to the future use of ICT in the agri-food sector, bioresource and biomass sector, EFITA’17, demonstration session, page 261, Montpellier, France, July 2017.

[93] Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzale´ Yeumo, Vincent Emonet, Valeria Pesce, and Pierre Larmande. AgroPortal: an open repository of ontologies and vocabularies for agriculture and nutrition data. In Ben Schaap, editor, GODAN Summit Open Data Research Symposium on Agriculture and Nutrition, GODAN’16, New York, NY, USA, September 2016.

[94] Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzale´Yeumo, Vincent Emonet, John Graybeal, Mark A. Musen, Cyril Pommier, and Pierre Larmande. Reusing the NCBO BioPortal technology for agronomy to build AgroPortal. In P. Jaiswal and R. Hoehndorf, editors, 7th International Conference on Biomedical Ontologies, ICBO’16, Demo Session, volume 1747 of CEUR Workshop Proceedings, page 3, Corvallis, Oregon, USA, August 2016.

[95] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. A Way to Automatically Enrich Biomedical Ontologies. In 19th International Conference on Extending Database Technology, EDBT’16, Poster Session, number 305, page 2, Bordeaux, France, March 2016. OpenProceedings.org.

[96] Clement Jonquet, Esther Dzale´-Yeumo, Elizabeth Arnaud, Pierre Larmande, Anne Toulet, and Marie-Ange´lique Laporte. AgroPortal: A Proposition for Ontology-Based Services in the Agronomic Domain. In 23rd Plant & Animal Genome Conference, poster session, page P0343, San Diego, USA, January 2016.

[97] Soumia Melzi and Clement Jonquet. Representing NCBO Annotator results in standard RDF with the Annotation Ontology. In A. Paschke, A. Burger, P. Romano, M.S. Marshall, and A. Splendiani, editors, 7th International Semantic Web Applications and Tools for Life Sciences poster session, SWAT4LS’14, volume 1320 of CEUR Workshop Proceedings, page 5, Berlin, Germany, December 2014. CEUR-WS.org.

[98] Aravind Venkatesan, Pierre Larmande, Clement Jonquet, Manuel Ruiz, and Patrick Valduriez. Facilitating efficient knowledge management and discovery in the Agronomic Sciences. In 4th Plenary Meeting of the Research Data Alliance, Amsterdam, The Netherlands, September 2014.

[99] Juan Antonio Lossio-Ventura, Clement Jonquet, Mathieu Roche, and Maguelonne Teisseire. BIOTEX: A system for Biomedical Terminology Extraction, Ranking, and Validation. In M. Horridge, M. Rospocher, and J. Ossenbruggen, editors, 13th International Semantic Web Conference, Demonstration, ISWC’14, volume 1272 of CEUR Workshop Proceedings, pages 157–160, Riva del Garda, Italy, October 2014.

[100]       Clement Jonquet, Christophe Fiorio, Philippe Papet, Ste´phanie Belin-Mejean, and ’Cellule iPad des enseignants de Polytech Montpellier’. Sce´narios pe´dagogiques nume´riques via l’utilisation de l’iPad par et pour les e´tudiants de Polytech Montpellier. In T. Karsenti, editor, 2e`me Sommet iPad en e´ducation, page 1, Montreal, Canada, May 2014. CRIFPE.

[101]       Emmanuel Castanier, Clement Jonquet, Soumia Melzi, Pierre Larmande, Manuel Ruiz, and Patrick Valduriez. Semantic Annotation Workflow using BioOntologies. In Workshop on Crop Ontology and Phenotyping Data Interoperability, Montpellier, France, April 2014. CGIAR.

[102]       Clement Jonquet. BioPortal : ontologies et ressources de donne´es biome´dicales a` porte´e de main. In L. Tamine, S. Darmoni, and L. Soualmia, editors, 1e`re e´dition du Symposium sur l’Inge´nierie de l’Information Me´dicale, SIIM’11, De´mos, Toulouse, France, June 2011.

[103]       Patricia L. Whetzel, Clement Jonquet, Cherie H. Youn, Michael Dorf, Ray Fergerson, Mark A. Musen, and Nigam H. Shah. The NCBO Annotator: OntologyBased Annotation as a Web Service. In Barry Smith, editor, International Conference on Biomedical Ontology, ICBO’11, Demonstration session, pages 302– 303, Buffalo, NY, USA, July 2011.

[104]       Patricia L. Whetzel, Nigam H. Shah, Natasha F. Noy, Clement Jonquet, Cherie H. Youn, Paul R. Alexander, Michael Dorf, and Mark A. Musen. Ontology-based Tools to Enhance the Curation Workflow. In 4th International Biocuration Conference, Poster Session, Tokyo, Japan, October 2010.

[105]       Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Clement Jonquet, Adrien Coulet, Cherie Youn, Michael Dorf, and Mark A. Musen. Ontology-based Web Services for Semantic Applications. In Bio-Ontologies: Semantic Applications in Life Sciences, SIG, Poster session, ISMB’10, Boston, MA, USA, July 2010.

[106]       Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Clement Jonquet, Adrien Coulet, Nicholas B. Griffith, Cherie H. Youn, Michael Dorf, and Mark A. Musen. Ontology Web Services for Semantic Applications. In Pacific Symposium on Biocomputing, Poster presentations, PSB’10, Hawaii, USA, January 2010.

[107]       Nigam H. Shah, Natasha F. Noy, Clement Jonquet, Adrien Coulet, Patricia L. Whetzel, Nicholas B. Griffith, Cherie H. Youn, Benjamin Dai, Michael Dorf, and Mark A. Musen. Ontology Services for Semantic Applications in Health and Life Sciences. In American Medical Informatics Association Annual Symposium, Demonstrations, AMIA’09, Washington DC, USA, November 2009.

[108]       Clement Jonquet, Nigam H. Shah, Cherie H. Youn, Chris Callendar, MargaretAnne Storey, and Mark A. Musen. NCBO Annotator: Semantic Annotation of Biomedical Data. In 8th International Semantic Web Conference, Poster and Demonstration Session, ISWC’09, Washington DC, USA, November 2009.

[109]       Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Cherie H. Youn, Chris Callendar, Adrien Coulet, Daniel L. Rubin, Barry Smith, Margaret-Anne Storey, Christopher G. Chute, and Mark A. Musen. BioPortal: Ontologies and Integrated Data Resources at the Click of the Mouse. In B. Smith, editor, International Conference on Biomedical Ontology, ICBO’09, page 197, Buffalo, NY, USA, July 2009.

[110]       Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Cherie H. Youn, Adrien Coulet, Chris Callendar, Daniel L. Rubin, Barry Smith, Margaret-Anne Storey, Christopher G. Chute, and Mark A. Musen. BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse. In Bio-Ontologies: Knowledge in Biology, SIG, Poster session, ISMBECCB’09, Stockholm, Sweden, July 2009.

[111]       Patricia L. Whetzel, Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Cherie H. Youn, Daniel L. Rubin, and Mark A. Musen. BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse. In 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB’09) and the 8th European Conference on Computational Biology (ECCB’09), Poster session, Stockholm, Sweden, July 2009.

[112]       Patricia L. Whetzel, Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Cherie H. Youn, Michael J. Montegut, Daniel L. Rubin, Margaret-Anne Storey, Chris G. Chute, and Mark A. Musen. BioPortal: A Web Repository for Biomedical Ontologies and Data Resources. In 3rd International Biocuration Conference, Poster presentations, page 97, Berlin, Germany, April 2009.

[113]       Simon N. Twigger, Jennifer Smith, Rajni Nigam, Clement Jonquet, and Mark A. Musen. Billion Data Points Trapped in International Data Repository Daring rescue Planned! In 3rd International Biocuration Conference, Poster presentations, page 34, Berlin, Germany, April 2009.

[114]       Patricia L. Whetzel, Natasha F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Michael J. Montegut, Daniel L. Rubin, Cherie H. Youn, and Mark A. Musen. BioPortal: A Web Repository for Biomedical Ontologies and Ontology-indexed Data Resources. In Pacific Symposium on Biocomputing, Poster presentations, PSB’09, page 90, Hawaii, USA, January 2009.

[115]       Mark A. Musen, Nigam H. Shah, Natasha F. Noy, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, James Buntrock, Clement Jonquet, Michael Montegut, and Daniel L. Rubin. BioPortal: Ontologies and Data Resources with the Click of a Mouse. In American Medical Informatics Association Annual Symposium, Demonstrations, AMIA’08, pages 1223–1224, Washington DC, USA, November 2008.

[116]       Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas B. Griffith, Clement Jonquet, Michael Montegut, Daniel L. Rubin, Cherie Youn, and Mark A. Musen. BioPortal: A Web Repository for Biomedical Ontologies and Data Resources. In C. Bizer and A. Joshi, editors, 7th International Semantic Web Conference, Poster and Demonstration Session, ISWC’08, volume 401 of CEUR Workshop Proceedings, Karlsruhe, Germany, October 2008. CEURWS.org.

Report

[117]       Anne Toulet, Biswanath Dutta, and Clement Jonquet. Assessing the Practice of Ontology Metadata: A Survey Result. Report, University of Montpellier and Indian Statistical Institute, Montpellier, France, June 2018. This report is a result from the RDA VISSIG Ontology Metadata task group.

[118]       Valeria Pesce, Jeni Tennison, Lisette Mey, Clement Jonquet, Anne Toulet, Sophie Aubin, and Panagiotis Zervas. A Map of Agri-food Data Standards. F1000 Research Technical Report 7-177, Global Open Data for Agriculture and Nutrition (GODAN), February 2018. Not peer reviewed.

[119]       Amina Annane, Zohra Bellahsene, Faical Azouaou, and Clement Jonquet. YAM-BIO – Results for OAEI 2017. System paper, LIRMM, University of Montpellier, Montpellier, France, November 2017. Ontology Alignment Evaluation Initiative 2017 Campaign.

[120]       Clement Jonquet, Mark A. Musen, and Nigam H. Shah. Help will be provided for this task: Ontology-Based Annotator Web Service. Research report BMIR2008-1317, Stanford University, CA, USA, May 2008.

[121]       Nigam H. Shah, Clement Jonquet, and Mark A. Musen. Ontrez project report. Research report BMIR-2007-1289, Stanford University, CA, USA, November 2007.

[122]       Clement Jonquet and Stefano A. Cerri. Characterization of the Dynamic Service Generation concept. Research report 06007, University Montpellier 2, France, February 2006.

[123]       Clement Jonquet. A framework and ontology for Semantic Grid services: an integrated view of WSMF and WSRF. Unpublished draft research report, University Montpellier 2 and KMi, Open University, France, May 2005.

Under Review or in Progress

[CJ-UR1] Romain David, Laurence Mabile (…), Clement Jonquet, (…) and Research Data Alliance - SHAring Reward & Credit (SHARC) Interest Group, FAIRness Literacy: the Achilles’ Heel of Applying FAIR Principles, Data Science Journal, Codata / Unbiquity Press, 2020.

[CJ-UR2] Mehdi Mirzapour, Amine Abdaoui, Andon Tchechmedjiev, William Digan, Sandra Bringay, Clement Jonquet, French ConText: a Publicly Accessible System for Detecting Negation, Temporality and Experiencer in French Clinical Notes, Biomedical Informatics, under review - JBI-18-620 – 3rd round, 2020.

[CJ-UR3] Amina Annane, Zohra Bellahsene, Faiçal Azouaou, Clement Jonquet, Using Background Knowledge to Enhance Ontology Matching: a Survey, Semantic Web, Rejected - 1525-2737, then 1662-2874, to be resubmitted, 2020.

Detailed ResEarch activity

Focus on HDR (habilitation) synthesis (2019)

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.

Research Projects (2003-2023)

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 workshop (a.k.a datathon), 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 will be 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) brings 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), shall allow 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) are used as demonstrators.

My contributions, within the “Conception” work-package, are 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 106 vocabularies with more than 2/3 of them not present in any similar ontology repository and 10 private ontologies. We have identified 80 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 4 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 is 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 extract state-of-the-art knowledge from PGx databases (PharmGKB) and literature (PubMed), and we extract observational knowledge from clinical data; then we compare 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, brings together two informatics labs: LORIA (Nancy) & LIRMM (Montpellier); and two hospitals: HEGP (Paris) and CHU St Etienne. At LIRMM, we are enhancing 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.