#ehealth #innovation #artificialintelligence #datascience

Rémy Choquet, PhD, is a e-health expert for data driven large scale projects. He has an excellent knowledge of local, national and european e-health issues. Besides, he is associated with the biggest e-health research lab in France which collaborates within many national or european H2020 projects.

He has a PhD in Public Health : Epidemiology and Medical data science from the Pierre and Marie Curie University (P6).

He actually is the medical data and personalized healthcare head at Roche Pharma France and member of the LIMICS lab (U1142) at INSERM. He is an expert in medical data science, semantics, data quality and interoperability in healthcare generated data reuse for public health and research (epidemiology and surveillance systems). He publishes into key domain specific journals and is often appointed as expert for national or european authorities for various e-health topics.

He was co-editor of the clinical research informatics section of the IMIA yearbook of medical informatics (2012-2017). He is french ANR health informatics project external expert reviewer. He participates to several journals or conferences as an external scientific reviewer. He is lecturer for registries and rare diseases. He teaches data science, big data and ontology engineering at the Lyon 2 university.

He’s main interests are : e-health strategy thinking, artificial intelligence, innovation, health information systems, data science, medical informatics, health informatics, clinical research informatics, ontologies, data quality, data integration, semantic interoperability, public health, rare diseases, health IT strategy, management, data privacy.

• J. Kedra, T. Radstake, A. Pandit, X. Baraliakos, F. Berenbaum, A. Finckh, B. Fautrel, T. A. Stamm, D. Gomez-Cabrero, C. Pristipino, R. Choquet, H. Servy, S. Stones, G. Burmester, and L. Gossec, « Current status of use of big data and artificial intelligence in RMDs: a systematic literature review informing EULAR recommendations., » Rmd open, vol. 5, iss. 2, p. e001004, 2019.
  [Bibtex]

  @article{Kedra2019,
  abstract = {Objective: To assess the current use of big data and artificial intelligence (AI) in the field of rheumatic and musculoskeletal diseases (RMDs). Methods: A systematic literature review was performed in PubMed MEDLINE in November 2018, with key words referring to big data, AI and RMDs. All original reports published in English were analysed. A mirror literature review was also performed outside of RMDs on the same number of articles. The number of data analysed, data sources and statistical methods used (traditional statistics, AI or both) were collected. The analysis compared findings within and beyond the field of RMDs. Results: Of 567 articles relating to RMDs, 55 met the inclusion criteria and were analysed, as well as 55 articles in other medical fields. The mean number of data points was 746 million (range 2000-5 billion) in RMDs, and 9.1 billion (range 100 000-200 billion) outside of RMDs. Data sources were varied: in RMDs, 26 (47{\%}) were clinical, 8 (15{\%}) biological and 16 (29{\%}) radiological. Both traditional and AI methods were used to analyse big data (respectively, 10 (18{\%}) and 45 (82{\%}) in RMDs and 8 (15{\%}) and 47 (85{\%}) out of RMDs). Machine learning represented 97{\%} of AI methods in RMDs and among these methods, the most represented was artificial neural network (20/44 articles in RMDs). Conclusions: Big data sources and types are varied within the field of RMDs, and methods used to analyse big data were heterogeneous. These findings will inform a European League Against Rheumatism taskforce on big data in RMDs.},
  author = {Kedra, Joanna and Radstake, Timothy and Pandit, Aridaman and Baraliakos, Xenofon and Berenbaum, Francis and Finckh, Axel and Fautrel, Bruno and Stamm, Tanja A and Gomez-Cabrero, David and Pristipino, Christian and Choquet, Remy and Servy, Herve and Stones, Simon and Burmester, Gerd and Gossec, Laure},
  doi = {10.1136/rmdopen-2019-001004},
  issn = {2056-5933 (Print)},
  journal = {RMD open},
  language = {eng},
  number = {2},
  pages = {e001004},
  pmid = {31413871},
  title = {{Current status of use of big data and artificial intelligence in RMDs: a systematic literature review informing EULAR recommendations.}},
  volume = {5},
  year = {2019}
  }

• L. Gossec, J. Kedra, H. Servy, A. Pandit, S. Stones, F. Berenbaum, A. Finckh, X. Baraliakos, T. A. Stamm, D. Gomez-Cabrero, C. Pristipino, R. Choquet, G. R. Burmester, and T. R. D. J. Radstake, « EULAR points to consider for the use of big data in rheumatic and musculoskeletal diseases., » Annals of the rheumatic diseases, 2019.
  [Bibtex]

  @article{Gossec2019,
  abstract = {BACKGROUND: Tremendous opportunities for health research have been unlocked by the recent expansion of big data and artificial intelligence. However, this is an emergent area where recommendations for optimal use and implementation are needed. The objective of these European League Against Rheumatism (EULAR) points to consider is to guide the collection, analysis and use of big data in rheumatic and musculoskeletal disorders (RMDs). METHODS: A multidisciplinary task force of 14 international experts was assembled with expertise from a range of disciplines including computer science and artificial intelligence. Based on a literature review of the current status of big data in RMDs and in other fields of medicine, points to consider were formulated. Levels of evidence and strengths of recommendations were allocated and mean levels of agreement of the task force members were calculated. RESULTS: Three overarching principles and 10 points to consider were formulated. The overarching principles address ethical and general principles for dealing with big data in RMDs. The points to consider cover aspects of data sources and data collection, privacy by design, data platforms, data sharing and data analyses, in particular through artificial intelligence and machine learning. Furthermore, the points to consider state that big data is a moving field in need of adequate reporting of methods and benchmarking, careful data interpretation and implementation in clinical practice. CONCLUSION: These EULAR points to consider discuss essential issues and provide a framework for the use of big data in RMDs.},
  author = {Gossec, Laure and Kedra, Joanna and Servy, Herve and Pandit, Aridaman and Stones, Simon and Berenbaum, Francis and Finckh, Axel and Baraliakos, Xenofon and Stamm, Tanja A and Gomez-Cabrero, David and Pristipino, Christian and Choquet, Remy and Burmester, Gerd R and Radstake, Timothy R D J},
  doi = {10.1136/annrheumdis-2019-215694},
  issn = {1468-2060 (Electronic)},
  journal = {Annals of the rheumatic diseases},
  language = {eng},
  month = {jun},
  pmid = {31229952},
  title = {{EULAR points to consider for the use of big data in rheumatic and musculoskeletal diseases.}},
  year = {2019}
  }

• M. Maaroufi, P. Landais, C. Messiaen, M. Jaulent, and R. Choquet, « Federating patients identities: the case of rare diseases., » Orphanet journal of rare diseases, vol. 13, iss. 1, p. 199, 2018.
  [Bibtex]

  @article{Maaroufi2018,
  abstract = {BACKGROUND: Patient information in rare disease registries is generally collected from numerous data sources, necessitating the data to be federated. In addition, data for research purposes must be de-identified. Transforming nominative data into de-identified data is thus a key issue, while minimizing the number of identity duplicates. We propose a method enabling patient identity federation and rare disease data de-identification while preserving the pertinence of the provided data. RESULTS: We developed a rare disease patient identifier. The IdMR generation process is a three-phased algorithm involving a hash function to irreversibly de-identify nominative patient data, including those of foetuses. This process minimizes collision risks and reduces variability for the purpose of identity federation. The IdMR was generated for 360,000 patients of the CEMARA database. It allowed identity federation of 1771 duplicated files. No collisions were introduced. CONCLUSION: We examined and discussed the risks of collisions and the creation of duplicates as well as the risks of patient re-identification. We discussed our choice of nominative input information in light of that used by other patient identification solutions. The IdMR is a patient identifier that enables identity federation and file linkage. The simplicity of the algorithm and the universality and stability of the input data make it a good candidate for European cross-border rare disease projects.},
  author = {Maaroufi, Meriem and Landais, Paul and Messiaen, Claude and Jaulent, Marie-Christine and Choquet, Remy},
  doi = {10.1186/s13023-018-0948-6},
  issn = {1750-1172 (Electronic)},
  journal = {Orphanet journal of rare diseases},
  keywords = {Algorithms,Databases, Factual,Humans,Rare Diseases},
  language = {eng},
  month = {nov},
  number = {1},
  pages = {199},
  pmid = {30419918},
  title = {{Federating patients identities: the case of rare diseases.}},
  volume = {13},
  year = {2018}
  }

• M. Jaulent, D. Leprovost, J. Charlet, and R. Choquet, « Semantic interoperability challenges to process large amount of data perspectives in forensic and legal medicine, » Journal of forensic and legal medicine, 2018.
  [Bibtex]

  @article{Jaulent2016,
  author = {Jaulent, Marie-Christine and Leprovost, Damien and Charlet, Jean and Choquet, Remy},
  doi = {10.1016/j.jflm.2016.10.002},
  issn = {1752928X},
  journal = {Journal of Forensic and Legal Medicine},
  keywords = {Forensic science,Knowledge engineering,Ontology,Semantic interoperability,Variety in big data},
  language = {English},
  month = {oct},
  publisher = {Elsevier},
  title = {{Semantic interoperability challenges to process large amount of data perspectives in forensic and legal medicine}},
  url = {http://www.jflmjournal.org/article/S1752928X1630124X/fulltext},
  year = {2018}
  }

• L. Friedlander, R. Choquet, E. Galliani, M. {De Chalendar}, C. Messiaen, A. Ruel, M. -P. Vazquez, A. Berdal, C. Alberti, and M. {De La Dure Molla}, « Management of rare diseases of the Head, Neck and Teeth: Results of a French population-based prospective 8-year study, » Orphanet journal of rare diseases, vol. 12, iss. 1, 2017.
  [Bibtex]

  @article{Friedlander2017,
  abstract = {{\textcopyright} 2017 The Author(s). Background: In the last ten years, national rare disease networks have been established in France, including national centres of expertise and regional ones, with storage of patient data in a bioinformatics tool. The aim was to contribute to the development and evaluation of health strategies to improve the management of patients with rare diseases. The objective of this study has been to provide the first national-level data concerning rare diseases of the head, neck and teeth and to assess the balance between demand and supply of care in France. Methods: Centres of expertise for rare diseases record a minimum data set on their clinical cases, using a list of rare Head, Neck and Teeth diseases established in 2006. The present analysis focuses on 2008 to 2015 data based on the Orphanet nomenclature. Each rare disease RD "case" was defined by status "affected" and by the degree of diagnostic certainty, encoded as: confirmed, probable or non-classifiable. Analysed parameters, presented with their 95{\%} confidence intervals using a Poisson model, were the following: time and age at diagnosis, proportions of crude and standardized RD prevalence by age, gender and geographical site. The criteria studied were the proportions of patients in Paris Region and the "included cases geography", in which these proportions were projected onto the other French Regions, adjusting for local populations. Results: In Paris Region, estimated prevalence of these diseases was 5.58 per 10,000 inhabitants (95{\%} CI 4.3-7.1). At December 31st 2015, 11,342 patients were referenced in total in France, of whom 7294 were in Paris Region. More than 580 individual clinical entities (ORPHA code) were identified with their respective frequencies. Most abnormalities were diagnosed antenatally. Nearly 80{\%} of patients recorded come to Paris hospitals to obtain either diagnosis, care or follow up. We observed that the rarer the disease, the more patients were referred to Paris hospitals. Conclusions: A health network covering a range of aspects of the rare diseases problematic from diagnostics to research has been developed in France. Despite this, there is still a noticeable imbalance between health care supply and demand in this area.},
  author = {Friedlander, L. and Choquet, R. and Galliani, E. and {De Chalendar}, M. and Messiaen, C. and Ruel, A. and Vazquez, M.-P. and Berdal, A. and Alberti, C. and {De La Dure Molla}, M.},
  doi = {10.1186/s13023-017-0650-0},
  file = {::},
  issn = {17501172},
  journal = {Orphanet Journal of Rare Diseases},
  keywords = {Epidemiology,Oral cleft,Orofacial diseases,Rare diseases,Registry},
  number = {1},
  title = {{Management of rare diseases of the Head, Neck and Teeth: Results of a French population-based prospective 8-year study}},
  volume = {12},
  year = {2017}
  }

• G. Baujat, R. Choquet, S. Bouée, V. Jeanbat, L. Courouve, A. Ruel, C. Michot, K. -H. {Le Quan Sang}, D. Lapidus, C. Messiaen, P. Landais, and V. Cormier-Daire, « Prevalence of fibrodysplasia ossificans progressiva (FOP) in France: An estimate based on a record linkage of two national databases, » Orphanet journal of rare diseases, vol. 12, iss. 1, 2017.
  [Bibtex]

  @article{Baujat2017,
  abstract = {{\textcopyright} 2017 The Author(s). Background: Fibrodysplasia ossificans progressiva (FOP) is a rare, severely disabling, and life-shortening genetic disorder that causes the formation of heterotopic bone within soft connective tissue. Previous studies found that the FOP prevalence was about one in every two million lives. The aim of this study is to estimate the FOP prevalence in France by probabilistic record-linkage of 2 national databases: 1) the PMSI (Programme de m{\'{e}}dicalisation des syst{\`{e}}mes d'information), an administrative database that records all hospitalization activities in France and 2) CEMARA, a registry database developed by the French Centres of Reference for Rare Diseases. Results: Using a capture-recapture methodology to adjust the crude number of patients identified in both data sources, 89 FOP patients were identified, which results in a prevalence of 1.36 per million inhabitants (CI95{\%} = [1.10; 1.68]). FOP patients' mean age was 25 years, only 14.9{\%} were above 40 years, and 53{\%} of them were males. The first symptoms - beside toe malformations- occurred after birth for 97.3{\%} of them. Mean age at identified symptoms was 7 years and above 18 years for only 6.9{\%} of patients. Mean age at diagnosis was 10 years, and above 18 years for 14.9{\%} of the patients. FOP patients were distributed across France. Conclusions: Despite the challenge of ascertaining patients with rare diseases, we report a much higher prevalence of FOP in France than in previous studies elsewhere. We suggest that efforts to identify patients and confirm the diagnosis of FOP should be reinforced and extended at both national and European level.},
  author = {Baujat, G. and Choquet, R. and Bou{\'{e}}e, S. and Jeanbat, V. and Courouve, L. and Ruel, A. and Michot, C. and {Le Quan Sang}, K.-H. and Lapidus, D. and Messiaen, C. and Landais, P. and Cormier-Daire, V.},
  doi = {10.1186/s13023-017-0674-5},
  file = {::},
  issn = {17501172},
  journal = {Orphanet Journal of Rare Diseases},
  keywords = {Data bases,Epidemiology,Fibrodysplasia ossificans progressiva,Prevalence,Rare genetic diseases},
  number = {1},
  title = {{Prevalence of fibrodysplasia ossificans progressiva (FOP) in France: An estimate based on a record linkage of two national databases}},
  volume = {12},
  year = {2017}
  }

• C. Daniel and R. Choquet, « Clinical Research Informatics Contributions from 2015, » Yearbook of medical informatics, iss. 1, 2016.
  [Bibtex]

  @article{Daniel2016,
  abstract = {OBJECTIVES: To summarize key contributions to current research in the field of Clinical Research Informatics (CRI) and to select best papers published in 2015. METHOD: A bibliographic search using a combination of MeSH and free terms search over PubMed on Clinical Research Informatics (CRI) was performed followed by a double-blind review in order to select a list of candidate best papers to be then peer-reviewed by external reviewers. A consensus meeting between the two section editors and the editorial team was finally organized to conclude on the selection of best papers. RESULTS: Among the 579 returned papers published in the past year in the various areas of Clinical Research Informatics (CRI) - i) methods supporting clinical research, ii) data sharing and interoperability, iii) re-use of healthcare data for research, iv) patient recruitment and engagement, v) data privacy, security and regulatory issues and vi) policy and perspectives - the full review process selected four best papers. The first selected paper evaluates the capability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) to support the representation of case report forms (in both the design stage and with patient level data) during a complete clinical study lifecycle. The second selected paper describes a prototype for secondary use of electronic health records data captured in non-standardized text. The third selected paper presents a privacy preserving electronic health record linkage tool and the last selected paper describes how big data use in US relies on access to health information governed by varying and often misunderstood legal requirements and ethical considerations. CONCLUSIONS: A major trend in the 2015 publications is the analysis of observational, "nonexperimental" information and the potential biases and confounding factors hidden in the data that will have to be carefully taken into account to validate new predictive models. In addiction, researchers have to understand complicated and sometimes contradictory legal requirements and to consider ethical obligations in order to balance privacy and promoting discovery.},
  author = {Daniel, C. and Choquet, R.},
  issn = {23640502},
  journal = {Yearbook of medical informatics},
  keywords = {Medical informatics,biomedical research,clinical research informatics,patient selection,phenotyping},
  number = {1},
  title = {{Clinical Research Informatics Contributions from 2015}},
  year = {2016}
  }

• R. Choquet, C. Messiaen, A. Ruel, L. Faivre, S. Odent, A. Verloes, D. Lacombe, S. Manouvrier, N. Philip, P. Sarda, D. Geneviève, P. Edery, C. Francannet, A. Lapointe, C. Thauvin-Robinet, M. Gonzales, T. Attié, and P. Landais, « Epidémiologie des anomalies du développement en France : une expérience de 8 années., » in Assises de génétique, Lyon, France, 2016.
  [Bibtex]

  @inproceedings{Choquet2016,
  address = {Lyon, France},
  author = {Choquet, R{\'{e}}my and Messiaen, Claude and Ruel, Am{\'{e}}lie and Faivre, Laurence and Odent, Sylvie and Verloes, Alain and Lacombe, Didier and Manouvrier, Sylvie and Philip, Nicole and Sarda, Pierre and Genevi{\`{e}}ve, David and Edery, Patrick and Francannet, Christine and Lapointe, Anne-Sophie and Thauvin-Robinet, Christel and Gonzales, Marie and Atti{\'{e}}, Tania and Landais, Paul},
  booktitle = {Assises de g{\'{e}}n{\'{e}}tique},
  file = {::},
  title = {{Epid{\'{e}}miologie des anomalies du d{\'{e}}veloppement en France : une exp{\'{e}}rience de 8 ann{\'{e}}es.}},
  year = {2016}
  }

• G. Baujat, C. Messiaen, S. Bouée, V. Cormier-Daire, V. Jeanbat, K. Le, Q. Sang, A. Ruel, C. Michot, D. Lapidus, P. Landais, and R. Choquet, « Prévalence de la fibrodysplasie ossifiante progressive (FOP) en France Estimation à partir de deux bases de données, » in Assises de génétique, Lyon, France, 2016.
  [Bibtex]

  @inproceedings{Baujat2016,
  abstract = {Au 01/01/2012, 85 patients vivants sont identifi{\'{e}}s FOP dans CEMARA et r{\'{e}}sident en France. Pour 63, le diagnostic avait {\'{e}}t{\'{e}} confirm{\'{e}} {\`{a}} cette date, 10 avaient d{\'{e}}j{\`{a}} des sympt{\^{o}}mes mais sans diagnostic confirm{\'{e}}. Pour le reste (N=12), ces donn{\'{e}}es sont manquantes.},
  address = {Lyon, France},
  author = {Baujat, Genevi{\`{e}}ve and Messiaen, Claude and Bou{\'{e}}e, St{\'{e}}phane and Cormier-Daire, Val{\'{e}}rie and Jeanbat, Viviane and Le, Kim-Hanh and Sang, Quan and Ruel, Am{\'{e}}lie and Michot, Caroline and Lapidus, David and Landais, Paul and Choquet, R{\'{e}}my},
  booktitle = {Assises de g{\'{e}}n{\'{e}}tique},
  file = {::},
  title = {{Pr{\'{e}}valence de la fibrodysplasie ossifiante progressive (FOP) en France Estimation {\`{a}} partir de deux bases de donn{\'{e}}es}},
  year = {2016}
  }

• M. Maaroufi, R. Choquet, P. Landais, and M. Jaulent, « Towards data integration automation for the French rare disease registry, » in American medical informatics association annual conference, 2015, p. in press.
  [Bibtex]

  @inproceedings{Maaroufi2015,
  abstract = {Building a medical registry upon an existing infrastructure and rooted practices is not an easy task. It is the case for the BNDMR project, the French rare disease registry, that aims to collect administrative and medical data of rare disease patients seen in different hospitals. To avoid duplicating data entry for health professionals, the project plans to deploy connectors with the existing systems to automatically retrieve data. Given the data heterogeneity and the large number of source systems, the automation of connectors creation is required. In this context, we propose a methodology that optimizes the use of existing alignment approaches in the data integration processes. The generated mappings are formalized in exploitable mapping expressions. Following this methodology, a process has been experimented on specific data types of a source system: Boolean and predefined lists. As a result, effectiveness of the used alignment approach has been enhanced and more good mappings have been detected. Nonetheless, further improvements could be done to deal with the semantic issue and process other data types.},
  author = {Maaroufi, Meriem and Choquet, Remy and Landais, Paul and Jaulent, Marie-Christine},
  booktitle = {American Medical Informatics Association Annual Conference},
  pages = {in press},
  title = {{Towards data integration automation for the French rare disease registry}},
  year = {2015}
  }

• R. Choquet, M. Maaroufi, Y. Fonjallaz, A. de Carrara, P. Vandenbussche, F. Dhombres, and P. Landais, « LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems, » in American medical informatics association annual conference, 2015, p. in press.
  [Bibtex]

  @inproceedings{Choquet2015a,
  abstract = {Characterizing a rare disease diagnosis for a given patient is often made through expert's networks. It is a complex task that could evolve over time depending on the natural history of the disease and the evolution of the scientific knowledge. Most rare diseases have genetic causes and recent improvements of sequencing techniques contribute to the discovery of many new diseases every year. Diagnosis coding in the rare disease field requires data from multiple knowledge bases to be aggregated in order to offer the clinician a global information space from possible diagnosis to clinical signs (phenotypes) and known genetic mutations (genotype). Nowadays, the major barrier to the coding activity is the lack of consolidation of such information scattered in different classifications such as Orphanet, OMIM or HPO. The Linking Open data for Rare Diseases (LORD) Web portal we developed stands as the first attempt to fill this gap by offering an integrated view of 8.400 rare diseases linked to more than 14.500 signs and 3.270 genes. The application provides a browsing feature to navigate through the relationships between diseases, signs and genes, and some Application Programming Interfaces to help its integration in health information systems in routine.},
  author = {Choquet, Remy and Maaroufi, Meriem and Fonjallaz, Yannick and de Carrara, Albane and Vandenbussche, Pierre-Yves and Dhombres, Ferdinand and Landais, Paul},
  booktitle = {American Medical Informatics Association Annual Conference},
  pages = {in press},
  title = {{LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems}},
  year = {2015}
  }

• R. Choquet, M. Maaroufi, A. {De Carrara}, C. Messiaen, E. Luigi, and P. Landais, « The french minimum dataset for rare diseases (FHIR HL7 format), » Journal of the american medical informatics association, 2015.
  [Bibtex]

  @article{Choquet2015,
  author = {Choquet, Remy and Maaroufi, Meriem and {De Carrara}, Albane and Messiaen, Claude and Luigi, Emmanuel and Landais, Paul},
  file = {::},
  journal = {Journal of the American Medical Informatics Association},
  title = {{The french minimum dataset for rare diseases (FHIR HL7 format)}},
  year = {2015}
  }

• A. Weill, R. Choquet, J. Rudant, P. Ricordeau, C. Messiaen, F. Alla, and P. Landais, « Prévalence de la cystinose en France, observance du traitement et coûts directs pour l’assurance maladie : base de données de l’assurance maladie (SNIIRAM) et BNDMR, » in 7e colloque pep adelf afcros, 2015, p. 1–16.
  [Bibtex]

  @inproceedings{Weill2015,
  author = {Weill, A and Choquet, R and Rudant, J and Ricordeau, P and Messiaen, C and Alla, F and Landais, P},
  booktitle = {7e Colloque PEP ADELF AFCROs},
  file = {::},
  pages = {1--16},
  title = {{Pr{\'{e}}valence de la cystinose en France, observance du traitement et co{\^{u}}ts directs pour l'assurance maladie : base de donn{\'{e}}es de l'assurance maladie (SNIIRAM) et BNDMR}},
  year = {2015}
  }

• R. Choquet, M. Maaroufi, A. de Carrara, C. Messiaen, E. Luigi, and P. Landais, « A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research., » Journal of the american medical informatics association : jamia, p. 1–7, 2015.
  [Bibtex]

  @article{Choquet2014b,
  abstract = {BACKGROUND: Although rare disease patients make up approximately 6-8{\%} of all patients in Europe, it is often difficult to find the necessary expertise for diagnosis and care and the patient numbers needed for rare disease research. The second French National Plan for Rare Diseases highlighted the necessity for better care coordination and epidemiology for rare diseases. A clinical data standard for normalization and exchange of rare disease patient data was proposed. The original methodology used to build the French national minimum data set (F-MDS-RD) common to the 131 expert rare disease centers is presented. METHODS: To encourage consensus at a national level for homogeneous data collection at the point of care for rare disease patients, we first identified four national expert groups. We reviewed the scientific literature for rare disease common data elements (CDEs) in order to build the first version of the F-MDS-RD. The French rare disease expert centers validated the data elements (DEs). The resulting F-MDS-RD was reviewed and approved by the National Plan Strategic Committee. It was then represented in an HL7 electronic format to maximize interoperability with electronic health records. RESULTS: The F-MDS-RD is composed of 58 DEs in six categories: patient, family history, encounter, condition, medication, and questionnaire. It is HL7 compatible and can use various ontologies for diagnosis or sign encoding. The F-MDS-RD was aligned with other CDE initiatives for rare diseases, thus facilitating potential interconnections between rare disease registries. CONCLUSIONS: The French F-MDS-RD was defined through national consensus. It can foster better care coordination and facilitate determining rare disease patients' eligibility for research studies, trials, or cohorts. Since other countries will need to develop their own standards for rare disease data collection, they might benefit from the methods presented here.},
  author = {Choquet, R{\'{e}}my and Maaroufi, Meriem and de Carrara, Albane and Messiaen, Claude and Luigi, Emmanuel and Landais, Paul},
  doi = {10.1136/amiajnl-2014-002794},
  file = {::},
  issn = {1527-974X},
  journal = {Journal of the American Medical Informatics Association : JAMIA},
  pages = {1--7},
  pmid = {25038198},
  title = {{A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research.}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/25038198},
  year = {2015}
  }

• D. Schober, R. Choquet, K. Depraetere, F. Enders, P. Daumke, M. -C. Jaulent, D. Teodoro, E. Pasche, C. Lovis, and M. Boekera, « DebugIT: Ontology-mediated layered data integration for real-time antibiotics resistance surveillance, » in Ceur workshop proceedings, 2014.
  [Bibtex]

  @inproceedings{Schober2014b,
  abstract = {Antibiotics resistance poses a significant problem in today's hospital care. Although large amounts of resistance data are gathered locally, they can-not be compared globally due to format and access diversity.We present an ontology-based integration approach serving an EU project in making antibiotics resistance data semantically and geographically interopera-ble. We particularly focus on EU-wide clinical data integration for real-time an-tibiotic resistance surveillance. The data semantics is formalized by multiple layers of terminology-bound description logic ontologies. Local database-to-RDF (D2R) converters, normalizers and data wrapper ontologies render hospi-tal data accessible to SPARQL queries, which popu late a mediator layer. This semiformal data is then integrated and rendered comparable via formal OWL domain ontologies and rule-driven reasoning applications. The presented inte-gration layer enables clinical data miners to query over multiple hospitals which behave like one homogeneous 'virtual clinical information system'. We show how cross-site querying can be achieved across borders, languages and different data models. Aside the drawbacks, we elaborate on the unique advantages over comparable previous efforts, i.e. tackling real-time data access and scalability.},
  author = {Schober, D. and Choquet, R. and Depraetere, K. and Enders, F. and Daumke, P. and Jaulent, M.-C. and Teodoro, D. and Pasche, E. and Lovis, C. and Boekera, M.},
  booktitle = {CEUR Workshop Proceedings},
  issn = {16130073},
  keywords = {Anti-biotics resistance,Antibacterial drug resistance,Antibiotics,Data integration,Data linkage,Epidemiological monitoring,Infection monitoring,Interoperability,Ontology,Public health surveil-lance,Semantic web},
  title = {{DebugIT: Ontology-mediated layered data integration for real-time antibiotics resistance surveillance}},
  volume = {1320},
  year = {2014}
  }

• M. Maaroufi, R. Choquet, P. Landais, and M. -C. Jaulent, Formalizing Mappings to Optimize Automated Schema Alignment: Application to Rare Diseases, , 2014, vol. 205.
  [Bibtex]

  @book{Maaroufi2014a,
  abstract = {{\textcopyright} 2014 European Federation for Medical Informatics and IOS Press. In the era of data sharing and systems interoperability, the automation of data schema alignment has become a priority. Discovering data mappings is the aim of many alignment approaches that have been described in the literature and the effectiveness of which depends on data specifications. In this context, we propose a method for mappings formalization that allows automated data integration processes optimization. This method, involving both data element level and value element level, allows an automated inference of mappings expressed by rules. In this paper, we start by describing the methods used to achieve this mappings formalization. Then, we explain how it has been validated by characterizing data from two use cases. We end up by discussing the objectives of the proposed formalization.},
  author = {Maaroufi, M. and Choquet, R. and Landais, P. and Jaulent, M.-C.},
  booktitle = {Studies in Health Technology and Informatics},
  doi = {10.3233/978-1-61499-432-9-283},
  isbn = {9781614994312},
  issn = {18798365},
  keywords = {Data integration,interoperability,mappings formalization,medical informatics,schema alignment},
  title = {{Formalizing Mappings to Optimize Automated Schema Alignment: Application to Rare Diseases}},
  volume = {205},
  year = {2014}
  }

• D. Schober, R. Choquet, K. Depraetere, F. Enders, P. Daumke, C. Jaulent, D. Teodoro, E. Pasche, C. Lovis, and M. Boeker, « DebugIT : Ontology-mediated layered Data Integration for real-time Antibiotics Resistance Surveillance DebugIT : Ontology-mediated layered Data Integration, » in Semantic web applicaitons for life science (swat4ls), 2014.
  [Bibtex]

  @inproceedings{Schober2014a,
  author = {Schober, Daniel and Choquet, R{\'{e}}my and Depraetere, Kristof and Enders, Frank and Daumke, Philip and Jaulent, Christine and Teodoro, Douglas and Pasche, Emilie and Lovis, Christian and Boeker, Martin},
  booktitle = {Semantic Web Applicaitons for Life Science (SWAT4LS)},
  file = {::},
  number = {DECEMBER},
  title = {{DebugIT : Ontology-mediated layered Data Integration for real-time Antibiotics Resistance Surveillance DebugIT : Ontology-mediated layered Data Integration}},
  year = {2014}
  }

• D. Schober, R. Choquet, K. Depraetere, and F. Enders, « DebugIT : Ontology-mediated layered Data Integration for real-time Antibiotics Resistance Surveillance As reflected in the appearance of recent infection control projects such as Infection-, » in Semantic web applicaitons for life science (swat4ls), 2014.
  [Bibtex]

  @inproceedings{Schober2014,
  author = {Schober, Daniel and Choquet, Remy and Depraetere, Kristof and Enders, Frank},
  booktitle = {Semantic Web Applicaitons for Life Science (SWAT4LS)},
  file = {::},
  number = {0},
  title = {{DebugIT : Ontology-mediated layered Data Integration for real-time Antibiotics Resistance Surveillance As reflected in the appearance of recent infection control projects such as Infection-}},
  year = {2014}
  }

• R. Choquet and P. Landais, « The French national registry for rare diseases: an integrated model from care to epidemiology and research, » Orphanet journal of rare diseases, vol. 9, iss. Suppl 1, p. O7, 2014.
  [Bibtex]

  @article{Choquet2014a,
  author = {Choquet, R{\'{e}}my and Landais, Paul},
  doi = {10.1186/1750-1172-9-S1-O7},
  file = {::},
  issn = {1750-1172},
  journal = {Orphanet Journal of Rare Diseases},
  number = {Suppl 1},
  pages = {O7},
  title = {{The French national registry for rare diseases: an integrated model from care to epidemiology and research}},
  url = {http://www.ojrd.com/content/9/S1/O7},
  volume = {9},
  year = {2014}
  }

• D. Taruscio, L. Vittozzi, R. Choquet, K. Heimdal, G. Iskrov, Y. Kodra, P. Landais, M. Posada, R. Stefanov, C. Steinmueller, E. Swinnen, and H. {Van Oyen}, « National Registries of Rare Diseases in Europe: An Overview of the Current Situation and Experiences, » Public health genomics, 2014.
  [Bibtex]

  @article{Taruscio2014,
  author = {Taruscio, D. and Vittozzi, L. and Choquet, R. and Heimdal, K. and Iskrov, G. and Kodra, Y. and Landais, P. and Posada, M. and Stefanov, R. and Steinmueller, C. and Swinnen, E. and {Van Oyen}, H.},
  doi = {10.1159/10.1159/000365897},
  issn = {1662-8063},
  journal = {Public Health Genomics},
  keywords = {EPIRARE,Epidemiology,Public health,Rare diseases,Registries},
  language = {english},
  publisher = {Karger Publishers},
  title = {{National Registries of Rare Diseases in Europe: An Overview of the Current Situation and Experiences}},
  url = {http://www.karger.com/Article/FullText/365897},
  year = {2014}
  }

• C. Daniel, R. Choquet, S. Editors, and I. Yearbook, « Information Technology for Clinical , Translational and Comparative Effectiveness Research Findings from the Section Clinical Research Informatics, » Yearbook of medical informatics, p. 1–7, 2014.
  [Bibtex]

  @article{Daniel2014,
  author = {Daniel, C and Choquet, R and Editors, Section and Yearbook, Imia},
  file = {::;::},
  journal = {Yearbook of medical informatics},
  keywords = {biomedical research,clinical research,international medical informatics associa-,medical informatics,nursing,patient selection,pharmacovigilance,phenotyping,research,tion,yearbook},
  pages = {1--7},
  title = {{Information Technology for Clinical , Translational and Comparative Effectiveness Research Findings from the Section Clinical Research Informatics}},
  year = {2014}
  }

• M. Maaroufi, R. Choquet, and P. Landais, « Formalizing mappings to optimize automated schema alignment : application to rare diseases, » in Medical informatics in europe (mie), 2014.
  [Bibtex]

  @inproceedings{Maaroufi2014,
  author = {Maaroufi, Meriem and Choquet, R{\'{e}}my and Landais, Paul},
  booktitle = {Medical Informatics in Europe (MIE)},
  file = {::},
  keywords = {data integration,formalization,interoperability,mappings,medical informatics,schema alignment},
  title = {{Formalizing mappings to optimize automated schema alignment : application to rare diseases}},
  year = {2014}
  }

• R. Choquet, Y. Fonjallaz, A. D. Carrara, M. Maaroufi, P. Vandenbussche, F. Dhombres, and P. Landais, « Coding rare diseases in health information systems : a tool for visualizing classifications and integrating phenotypic and genetic data, » in Journées francofones de l’informatique médicale (jfim), 2014.
  [Bibtex]

  @inproceedings{Choquet2014,
  abstract = {Establishing the diagnosis and coding for a rare disease (RD) needs to characterize multiple information including patient's phenotype and genotype. A major barrier to coding is a lack of consolidation of such information, scattered in several resources such as Orphanet, OMIM or HPO. We developed a web portal, Linking Open data for RD (LORD), offering an integrated view of 8,336 RDs linked to more than 12,500 signs and 3,000 genes. It allows navigating through the relationships between diseases, signs and genes, and provides Application Programming Interfaces for its integration in information systems (IS). LORD is dedicated to the 131 French RD reference centers and 501 competence centers, for coding RD diagnoses in the health IS.},
  author = {Choquet, R{\'{e}}my and Fonjallaz, Yannick and Carrara, Albane De and Maaroufi, Meriem and Vandenbussche, Pierre-yves and Dhombres, Ferdinand and Landais, Paul},
  booktitle = {Journ{\'{e}}es Francofones de l'Informatique M{\'{e}}dicale (JFIM)},
  file = {::},
  title = {{Coding rare diseases in health information systems : a tool for visualizing classifications and integrating phenotypic and genetic data}},
  year = {2014}
  }

• R. Choquet, A. Assélé-Kama, J. Charlet, and M. -C. Jaulent, « Semantic interoperability for antimicrobial resistance surveillance solutions in Europe, » Ingenierie des systemes d’information, vol. 18, iss. 6, 2013.
  [Bibtex]

  @article{Choquet2013a,
  abstract = {This article deals with the problematic of biomedical information sharing in the study of antibioresistance growth in Europe. Our general working hypothesis is: how can we share biomedical information in Europe in a non ambiguous way, in a fast way, and on demand? Many issues are raised by this working hypothesis: the issue of the quality of the data, the issue of the representation of data through structure, vocabulary, and semantics. We also address the problem of alignment of data with domain ontologies and the problem of data mediation using domain ontologies. We then present a system of semantic interoperability based on rules addressing the problem of semantic alignment of heterogeneous systems applied to our domain. Finally we discuss how semantics can contribute to the improvement of information sharing and we also discuss the limits of the current tools and methods. {\textcopyright} 2013 Lavoisier.},
  author = {Choquet, R. and Ass{\'{e}}l{\'{e}}-Kama, A. and Charlet, J. and Jaulent, M.-C.},
  doi = {10.3166/isi.18.6.59-82},
  issn = {21167125},
  journal = {Ingenierie des Systemes d'Information},
  keywords = {Data integration,Data quality,Data warehouse,Information models,Medical informatics,Ontologies,Query rewriting,Semantic interoperability,Semantic mediation,Semantic web,Standards},
  number = {6},
  title = {{Semantic interoperability for antimicrobial resistance surveillance solutions in Europe}},
  volume = {18},
  year = {2013}
  }

• R. Choquet, A. Assélé, J. Charlet, and M. Jaulent, « Solutions d’interopérabilité sémantique pour la surveillance de l’antibioresistance en Europe, » Rsti série ingénierie des systèmes d’information, vol. 18, iss. 6, 2013.
  [Bibtex]

  @article{Choquet2013,
  abstract = {Cet article traite de la probl{\'{e}}matique de partage de donn{\'{e}}es biom{\'{e}}dicales dans le cadre du suivi de l'{\'{e}}volution de la r{\'{e}}sistance des bact{\'{e}}ries aux antibiotiques en Europe. Dans ce domaine, les questions suivantes se posent : comment partager de l'information biom{\'{e}}dicale de mani{\`{e}}re non ambigu{\"{e}}, en temps r{\'{e}}el, et {\`{a}} la demande en Europe ? Ces questions sont associ{\'{e}}es {\`{a}} diverses probl{\'{e}}matiques telles que la qualit{\'{e}} des donn{\'{e}}es {\`{a}} partager, leur repr{\'{e}}sentation {\`{a}} travers leur structure, leur vocabulaire et leur s{\'{e}}mantique. Nous abordons aussi les probl{\`{e}}mes d'alignement de donn{\'{e}}es aux ontologies de domaine et de la f{\'{e}}d{\'{e}}ration de donn{\'{e}}es aid{\'{e}}e d'ontologies. Enfin, nous pr{\'{e}}sentons un syst{\`{e}}me d'interop{\'{e}}rabilit{\'{e}} s{\'{e}}mantique fond{\'{e}} sur des r{\`{e}}gles et qui aborde le probl{\`{e}}me de l'alignement s{\'{e}}mantique de syst{\`{e}}mes h{\'{e}}t{\'{e}}rog{\`{e}}nes appliqu{\'{e}} {\`{a}} notre domaine. Nous discutons finalement de l'apport de la s{\'{e}}mantique pour le partage d'information et des limites des outils et m{\'{e}}thodes actuels.},
  author = {Choquet, R{\'{e}}my and Ass{\'{e}}l{\'{e}}, Ariane and Charlet, Jean and Jaulent, Marie-Christine},
  file = {::},
  journal = {RSTI s{\'{e}}rie Ing{\'{e}}nierie des syst{\`{e}}mes d'information},
  keywords = {data integration,data quality,data warehouse,information models,medical informatics,ontologies,query rewriting,semantic interoperability,semantic mediation,semantic web,standards},
  mendeley-tags = {data integration,data quality,data warehouse,information models,medical informatics,ontologies,query rewriting,semantic interoperability,semantic mediation,semantic web,standards},
  number = {6},
  title = {{Solutions d'interop{\'{e}}rabilit{\'{e}} s{\'{e}}mantique pour la surveillance de l'antibioresistance en Europe}},
  volume = {18},
  year = {2013}
  }

• C. Daniel and R. Choquet, « Information technology for clinical, translational and comparative effectiveness research. Findings from the section clinical research informatics., » Yearbook of medical informatics, vol. 8, iss. 1, p. 185–9, 2013.
  [Bibtex]

  @article{Daniel2013,
  abstract = {OBJECTIVES: To summarize advances of excellent current research in the new emerging field of Clinical Research Informatics.
  METHOD: Synopsis of four key articles selected for the IMIA Yearbook 2013. The selection was performed by querying PubMed and Web of Science with predefined keywords. From the original set of 590 papers, a first subset of 461 articles which was in the scope of Clinical Research Informatics was refined into a second subset of 79 relevant articles from which 15 articles were retained for peer-review.
  RESULTS: The four selected articles exemplify current research efforts conducted in the areas of data representation and management in clinical trials, secondary use of EHR data for clinical research, information technology platforms for translational and comparative effectiveness research and implementation of privacy control.
  CONCLUSIONS: The selected articles not only illustrate how innovative information technology supports classically organized randomized controlled trials but also demonstrate that the long promised benefits of electronic health care data for research are becoming a reality through concrete platforms and projects.},
  author = {Daniel, C and Choquet, R},
  file = {::},
  issn = {0943-4747},
  journal = {Yearbook of medical informatics},
  month = {jan},
  number = {1},
  pages = {185--9},
  pmid = {23974570},
  title = {{Information technology for clinical, translational and comparative effectiveness research. Findings from the section clinical research informatics.}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/23974570},
  volume = {8},
  year = {2013}
  }

• A. Assélé, R. Choquet, G. Mels, C. Daniel, J. Charlet, and C. Jaulent, « An ontological approach for the exploitation of clinical data, » Medinfo, 2013.
  [Bibtex]

  @article{Assele2013,
  author = {Ass{\'{e}}l{\'{e}}, Ariane and Choquet, R{\'{e}}my and Mels, Giovanni and Daniel, Christel and Charlet, Jean and Jaulent, Christine},
  file = {::},
  journal = {MEDINFO},
  keywords = {database mapping,olap,ontology,rdf,semantic database,sparql endpoint},
  title = {{An ontological approach for the exploitation of clinical data}},
  year = {2013}
  }

• F. Dhombres, P. Vandenbussche, R. Choquet, X. Aimé, and J. Charlet, « The OntoOrpha Ontology – few Propositions to organize Orphanet Knowledge in the Semantic Web paradigm, » Special interest group imia for francophone members, 2013.
  [Bibtex]

  @article{Dhombres2013,
  author = {Dhombres, Ferdinand and Vandenbussche, Pierre-yves and Choquet, R{\'{e}}my and Aim{\'{e}}, Xavier and Charlet, Jean},
  file = {::},
  journal = {Special Interest Group IMIA for francophone members},
  keywords = {cuments de communication,doivent {\^{e}}tre actualis{\'{e}}s r{\'{e}}guli{\`{e}}rement,domain ontology,les an-,les cahiers d,nuaires,o rpha net,owl-dl,rare diseases,s parql,selon des don-},
  title = {{The OntoOrpha Ontology - few Propositions to organize Orphanet Knowledge in the Semantic Web paradigm}},
  year = {2013}
  }

• A. Assele, A. Primadhanty, R. Choquet, D. Teodoro, F. Enders, C. Duclos, and M. Jaulent, « Data Definition Ontology for clinical data integration and querying, » in Medical informatics in europe (mie), 2012.
  [Bibtex]

  @inproceedings{82,
  author = {Assele, Ariane and Primadhanty, Audi and Choquet, Remy and Teodoro, Douglas and Enders, Frank and Duclos, Catherine and Jaulent, Marie-Christine},
  booktitle = {Medical Informatics in Europe (MIE)},
  title = {{Data Definition Ontology for clinical data integration and querying}},
  year = {2012}
  }

• R. Choquet, S. Amselem, A. Clement, and P. Landais, « ISy-Rare : A French Information System for rare diseases, » in European conference for rare diseases (ecrd2012), Brussels, Belgium, 2012.
  [Bibtex]

  @inproceedings{79,
  abstract = {The French government has recently released a national plan to foster research about rare diseases and orphan pharmaceutical products. One axis aims at building an historical database that would help identifying rare disease patients on the French territory and help in gaining knowledge about the adequacy between demand and offer of care for rare diseases. A second axis is dedicated to promote the constitution of cohorts of patients presenting rare diseases and to evaluate innovative therapies.
  The data gathered by the 131 expert centres and 501 centres of competence are heterogeneous and incomplete. The objective is to build a coordinated collection of data, which will be annotated with the Orphanet terminology.
  Based on the existing French resources (data and knowledge), we propose to build a coherent organisation of the information about rare diseases on the French territory by federating them under a unique French information system for rare diseases. This information system will be fed by patient data, through expert centres, into a national rare disease patient identification system where each health professional will be able to declare and follow his/her patients. This system will be connected to electronic patient management systems (through standard interfaces) to avoid double data capture. This identification system will help in building epidemiological studies. It will allow identifying patients for inclusion in clinical trials. It will also be an information source for patient recruitment for cohorts and advanced research involving {\{}$\backslash$textendash{\}}omics and biobanks data. As a central key asset of our information system, we propose the use of advanced knowledge management systems to manage knowledge about rare diseases, -omics and clinical data. The independent management of data and knowledge will guarantee the sustainability of our information system.
  },
  address = {Brussels, Belgium},
  author = {Choquet, Remy and Amselem, Serge and Clement, Annick and Landais, Paul},
  booktitle = {European Conference for Rare Diseases (ECRD2012)},
  keywords = {french national plan,information system,rare disease},
  publisher = {ECRD 2012 : European conference for rare diseases},
  title = {{ISy-Rare : A French Information System for rare diseases}},
  type = {Poster},
  year = {2012}
  }

• R. Choquet, C. Messiaen, A. Priouzeau, A. {De Carrara}, P. Landais, and A. D. Carrara, « Un jeu de données minimum pour faciliter l’interopérabilité des bases de données pour les maladies rares, » in Ingénierie des connaissances (ic2012), 2012, p. 1–6.
  [Bibtex]

  @inproceedings{83,
  abstract = {La d{\{}{\'{e}}{\}}finition de vocabulaires ou de mod{\{}{\`{e}}{\}}les de donn{\{}{\'{e}}{\}}es communs apporte une aide importante pour garantir l{\{}$\backslash$textquoteright{\}}interop{\{}{\'{e}}{\}}rabilit{\{}{\'{e}}{\}} des syst{\{}{\`{e}}{\}}mes d{\{}$\backslash$textquoteright{\}}information en sant{\{}{\'{e}}{\}}. Dans le cadre de plans nationaux pour la mise en {\{}{\oe}{\}}uvre d{\{}$\backslash$textquoteright{\}}un syst{\{}{\`{e}}{\}}me d{\{}$\backslash$textquoteright{\}}information commun {\{}{\`{a}}{\}} toutes les maladies rares (environ 7000), nous proposons une m{\{}{\'{e}}{\}}thode permettant la d{\{}{\'{e}}{\}}finition d{\{}$\backslash$textquoteright{\}}un jeu de donn{\{}{\'{e}}{\}}es minimum (minimum dataset) pour les maladies rares. La d{\{}{\'{e}}{\}}finition d{\{}$\backslash$textquoteright{\}}un jeu d{\{}$\backslash$textquoteright{\}}{\{}{\'{e}}{\}}l{\{}{\'{e}}{\}}ments de donn{\{}{\'{e}}{\}}es commun minimum permet de s{\{}$\backslash$textquoteright{\}}assurer qu{\{}$\backslash$textquoteright{\}}un tronc commun d{\{}$\backslash$textquoteright{\}}{\{}{\'{e}}{\}}l{\{}{\'{e}}{\}}ment de donn{\{}{\'{e}}{\}}es partageables dans le domaine des maladies rares {\{}{\`{a}}{\}} l{\{}$\backslash$textquoteright{\}}{\{}{\'{e}}{\}}chelon national. Nous proposons une m{\{}{\'{e}}{\}}thodologie sp{\{}{\'{e}}{\}}cifique et nous publions les premiers r{\{}{\'{e}}{\}}sultats de notre {\{}{\'{e}}{\}}tude que nous discutons.},
  author = {Choquet, R{\'{e}}my and Messiaen, Claude and Priouzeau, Adrien and {De Carrara}, Albane and Landais, Paul and Carrara, Albane De},
  booktitle = {Ing{\'{e}}nierie des connaissances (IC2012)},
  file = {::},
  pages = {1--6},
  title = {{Un jeu de donn{\'{e}}es minimum pour faciliter l'interop{\'{e}}rabilit{\'{e}} des bases de donn{\'{e}}es pour les maladies rares}},
  volume = {2},
  year = {2012}
  }

• F. Dhombres, P. -Y. Vandenbussche, A. Rath, M. Hanauer, A. Olry, B. Urbero, R. Choquet, and J. Charlet, « Projet OrphaOnto – First stage of the ontologization of the ORPHANET knowledge bases, » in 22emes journees francophones d’ingenierie des connaissances, ic 2011, 2011.
  [Bibtex]

  @inproceedings{Dhombres2011,
  author = {Dhombres, F. and Vandenbussche, P.-Y. and Rath, A. and Hanauer, M. and Olry, A. and Urbero, B. and Choquet, R. and Charlet, J.},
  booktitle = {22emes Journees Francophones d'Ingenierie des Connaissances, IC 2011},
  title = {{Projet OrphaOnto - First stage of the ontologization of the ORPHANET knowledge bases}},
  year = {2011}
  }

• F. Dhombres, P. Vandenbussche, A. Rath, M. Hanauer, A. Orly, B. Urbero, R. Choquet, and J. Charlet, « Projet OrphaOnto – Première étape de l’ontologisation des bases de connaissances d’Orphanet, » in Actes des 22e journées francophones d’ingénierie des connaissances, 2011.
  [Bibtex]

  @inproceedings{74,
  author = {Dhombres, Ferdinand and Vandenbussche, Pierre-Yves and Rath, Anna and Hanauer, Marc and Orly, Annie and Urbero, Bruno and Choquet, Remy and Charlet, Jean},
  booktitle = {Actes des 22e Journ{\'{e}}es Francophones d'Ing{\'{e}}nierie des Connaissances},
  title = {{Projet OrphaOnto - Premi{\`{e}}re {\'{e}}tape de l'ontologisation des bases de connaissances d'Orphanet}},
  year = {2011}
  }

• F. Dhombres, P. Vandenbussche, A. Rath, M. Hanauer, A. Orly, B. Urbero, R. Choquet, and J. Charlet, « OntoOrpha : an ontology to support the editing and audit of rare diseases knowledge in Orphanet, » in International conference of biomedical ontology (icbo 2011), 2011.
  [Bibtex]

  @inproceedings{75,
  abstract = {Orphanet is the reference information portal on rare diseases and orphan drugs for all audience (for both healthcare professionals and general public). Orphanet is led by a large European consortium of around 40 countries, coordinated by the French INSERM team which is responsible for the infrastructure of Orphanet, the management tools, the quality control, the rare diseases inventory, the classifications and the edition of the encyclopedia*.
  After ten years of evolution, current Orphanet tools are limited in efficiently supporting the editing, update and data sharing processes of a constantly growing rare diseases knowledge (6000 rare diseases with annotations and more than one hundred overlapping classifications).},
  author = {Dhombres, Ferdinand and Vandenbussche, Pierre-Yves and Rath, Anna and Hanauer, Marc and Orly, Annie and Urbero, Bruno and Choquet, Remy and Charlet, Jean},
  booktitle = {International Conference of Biomedical Ontology (ICBO 2011)},
  title = {{OntoOrpha : an ontology to support the editing and audit of rare diseases knowledge in Orphanet}},
  year = {2011}
  }

• D. Teodoro, R. Choquet, D. Schober, G. Mels, E. Pasche, P. Ruch, and C. Lovis, « Interoperability driven integration of biomedical data sources, » in Xxiii international conference of the european federation for medical informatics (mie), 2011.
  [Bibtex]

  @inproceedings{72,
  abstract = {In this paper, we introduce a data integration methodology that promotes technical, syntactic and semantic interoperability for operational healthcare data sources. ETL processes provide access to different operational databases at the technical level. Furthermore, data instances have they syntax aligned according to biomedical terminologies using natural language processing. Finally, semantic web technologies are used to ensure common meaning and to provide ubiquitous access to the data. The system{\{}$\backslash$textquoteright{\}}s performance and solvability assessments were carried out using clinical questions against seven healthcare institutions distributed across Europe. The architecture managed to provide interoperability within the limited heterogeneous grid of hospitals. Preliminary scalability result tests are provided},
  author = {Teodoro, Douglas and Choquet, Remy and Schober, Daniel and Mels, Giovanni and Pasche, Emilie and Ruch, Patrick and Lovis, Christian},
  booktitle = {XXIII International Conference of the European Federation for Medical Informatics (MIE)},
  title = {{Interoperability driven integration of biomedical data sources}},
  year = {2011}
  }

• R. Choquet, C. Daniel, P. Grohs, N. Douali, and M. Jaulent, « Monitoring the emergence of antibiotic resistance using the technology ot the DebugIT platform in the HEGP context, » in International conference on prevention & infection control (icpic 2011), 2011.
  [Bibtex]

  @inproceedings{73,
  abstract = {This work takes part in the European DebugIT project which goal is to build a technical and semantic information technology platform able to share heterogeneous clinical data sets from different hospitals for the monitoring and the control of infectious diseases and antimicrobial resistances in Europe. The aim of the study is to compare the incidence rates of antimicrobial resistance at the HEGP hospital obtained in real-time by the DebugIT platform to those established by the yearly performed analysis processed by the microbiologists of the HEGP hospital.},
  author = {Choquet, Remy and Daniel, Christel and Grohs, Patrick and Douali, Nassim and Jaulent, Marie-Christine},
  booktitle = {International Conference on Prevention {\&} Infection Control (ICPIC 2011)},
  title = {{Monitoring the emergence of antibiotic resistance using the technology ot the DebugIT platform in the HEGP context}},
  year = {2011}
  }

• R. Choquet, D. Karlsson, D. Schober, P. Daumke, P. Ruch, D. Teodoro, G. Mels, A. Assele, D. Colaert, C. Lovis, M. Jaulent, H. Cools, and J. {De Roo}, « Exchanging biomedical information at large scale using the Semantic Web, » in Xxiii international conference of the european federation for medical informatics (mie), 2011.
  [Bibtex]

  @inproceedings{77,
  abstract = {In the biomedical field, the need for exchanging medical information across Europe to improve patient safety is increasing. In this workshop, we will showcase how Semantic Web technologies are used to build a large-scale surveillance system to monitor the emergence of antibiotic resistance in Europe. We will highlight methods to bind vocabularies and information models with domain on-tologies, and show how this contribute to interoperability and secondary data us-age within the DebugIT EU project.},
  author = {Choquet, Remy and Karlsson, Daniel and Schober, Daniel and Daumke, Philip and Ruch, Patrick and Teodoro, Douglas and Mels, Giovanni and Assele, Ariane and Colaert, Dirk and Lovis, Christian and Jaulent, Marie-Christine and Cools, Hans and {De Roo}, Jos},
  booktitle = {XXIII International Conference of the European Federation for Medical Informatics (MIE)},
  title = {{Exchanging biomedical information at large scale using the Semantic Web}},
  type = {Workshop},
  year = {2011}
  }

• C. Daniel, R. Choquet, A. Assele, F. Enders, P. Daumke, and M. Jaulent, « Comparing the DebugIT dashboards to national surveillance systems, » in International conference on prevention and infection control (icpic 2011), 2011.
  [Bibtex]

  @inproceedings{76,
  abstract = {An important limitation of existing large-scale surveillance systems of infectious diseases is that they use mostly manual data collection processes and therefore usually deliver trends on an annual basis. The DebugIT project, funded by the 7th EU Framework Programme, provides an access to heterogeneous clinical data sets of different European hospitals. We compared the DebugIT control capabilities to the process and results provided by the French surveillance system of infectious disease (Institut de Veille Sanitaire (InVS)) and the antimicrobial resistance surveillance study of the Paul-Ehrlich-Society (PEG).},
  author = {Daniel, Christel and Choquet, Remy and Assele, Ariane and Enders, Frank and Daumke, Philip and Jaulent, Marie-Christine},
  booktitle = {International Conference on Prevention and Infection Control (ICPIC 2011)},
  title = {{Comparing the DebugIT dashboards to national surveillance systems}},
  year = {2011}
  }

• R. Choquet, « Sharing biomedical information : models, semantics and quality, » Ingénierie de la connaissance en santé PhD Thesis, 2011.
  [Bibtex]

  @phdthesis{78,
  abstract = {The amount of available data in information systems is constantly increasing and more and more efforts have been made in trying to interconnect this data in order to gain knowledge or meaning. Yet, these attempts at interconnecting such data have never been satisfactory enough when it comes to using the information at a wider scale. The origins of such difficulties are manifold. First, information is represented in many different structures. Second, the vocabulary used to express data is heterogeneous. Finally, the quality of the information is often too poor to be used and to withdraw any knowledge from it. Such observation applies specifically to the biomedical area where it is still difficult to agree on a common and shared representation (structures and vocabulary) concerning a particular sub-domain of the medical field. It would appear difficult in such a context to solve the problem of information sharing by imposing standard coding and standard information models. More recently, the introduction of semantics in the process of information sharing enables us to setup pivots representations which are independent from the structure or from the naming of the data. This thesis deals with the problematics of biomedical information sharing in the study of antibiotics resistance evolution to bacteries in Europe. Our general working hypothesis is : how can we share biomedical information in Europe in a non ambiguous way, in a fast way, and on demand ? Many issues are raised by this working hypothesis. We will deal with the issue of the quality of the data, the issue of the representation of data through their structure, their vocabulary, their semantics. We will also address the problems of alignment of data with domain ontologies. And the problem of data mediation helped with domain ontologies. We will then present a system of semantic interoperability based on rules which addresses the problem of semantic alignment of heterogeneous systems applied to our domain. Finally we will discuss how semantics can contribute to the improvement of information sharing and we will also discuss the limits of the current tools and methods.},
  author = {Choquet, Remy},
  doi = {tel-00824931},
  keywords = {Data Integration,DebugIT,data quality,data warehouse,description logic,european project,information models,medical informatics,query rewriting,reasoning,rules,semantic interoperability,semantic mediation,semantic web},
  school = {Universit{\'{e}} Pierre et Marie Curie - Paris VI},
  title = {{Sharing biomedical information : models, semantics and quality}},
  type = {Ing{\'{e}}nierie de la connaissance en sant{\'{e}}},
  url = {http://www.remychoquet.fr/These.pdf https://tel.archives-ouvertes.fr/tel-00824931/},
  year = {2011}
  }

• R. Choquet, D. Teodoro, G. Mels, A. Assele, E. Pasche, P. Ruch, C. Lovis, and M. -C. Jaulent, « Sharing of biomedical data on the semantic web, » in Ceur workshop proceedings, 2010.
  [Bibtex]

  @inproceedings{Choquet2010a,
  author = {Choquet, R. and Teodoro, D. and Mels, G. and Assele, A. and Pasche, E. and Ruch, P. and Lovis, C. and Jaulent, M.-C.},
  booktitle = {CEUR Workshop Proceedings},
  issn = {16130073},
  title = {{Sharing of biomedical data on the semantic web}},
  volume = {600},
  year = {2010}
  }

• R. Choquet, S. Qouiyd, E. Pasche, C. Daniel, O. Boussaid, and M. -C. Jaulent, « A knowledge model to measure the quality of an information source, » in 21es journees francophones d’ingenierie des connaissances, ic 2010, 2010.
  [Bibtex]

  @inproceedings{Choquet2010,
  author = {Choquet, R. and Qouiyd, S. and Pasche, E. and Daniel, C. and Boussaid, O. and Jaulent, M.-C.},
  booktitle = {21es Journees Francophones d'Ingenierie des Connaissances, IC 2010},
  isbn = {9782911256257},
  title = {{A knowledge model to measure the quality of an information source}},
  year = {2010}
  }

• A. A. Kama, G. Mels, R. Choquet, J. Charlet, and M. -C. Jaulent, « An ontological approach to the exploitation of clinical data, » in 21es journees francophones d’ingenierie des connaissances, ic 2010, 2010.
  [Bibtex]

  @inproceedings{Kama2010,
  author = {Kama, A.A. and Mels, G. and Choquet, R. and Charlet, J. and Jaulent, M.-C.},
  booktitle = {21es Journees Francophones d'Ingenierie des Connaissances, IC 2010},
  isbn = {9782911256257},
  title = {{An ontological approach to the exploitation of clinical data}},
  year = {2010}
  }

• A. Assele, G. Mels, R. Choquet, and M. Jaulent, « Utilisation d’une ontologie comme source de données pour répondre à des questions cliniques, » in Ingénierie de la connaissance (ic2010), 2010.
  [Bibtex]

  @inproceedings{71,
  abstract = {L'utilisation des outils et techniques du web s{\'{e}}mantique pour int{\'{e}}grer, mod{\'{e}}liser et interroger des bases de donn{\'{e}}es relationnelles est un moyen de prendre en compte la dimension s{\'{e}}mantique des donn{\'{e}}es et d'en faciliter leur exploitation. Les donn{\'{e}}es issues des syst{\`{e}}mes hospitaliers peuvent {\{}{\^{e}}{\}}tre inexploitables dans leur format d'origine (qualit{\'{e}}, donn{\'{e}}es manquantes ou incompl{\`{e}}tes), il est donc n{\'{e}}cessaire dans certains cas d'exploiter des ressources externes aux bases de donn{\'{e}}es cliniques, comme compl{\'{e}}ment d'information, pour pallier ce probl{\`{e}}me. Nous proposons ici d'utiliser une ontologie comme source de donn{\'{e}}es pour r{\'{e}}pondre {\`{a}} des questions m{\'{e}}dicales dans le champ de l'antibior{\'{e}}sistance, en utilisant les standards et outils du web s{\'{e}}mantique. },
  author = {Assele, Ariane and Mels, Giovanni and Choquet, Remy and Jaulent, Marie-Christine},
  booktitle = {Ing{\'{e}}nierie de la Connaissance (IC2010)},
  keywords = {Entrep{\{}{\^{o}}{\}}ts de donn{\'{e}}es,Ontologie,RDF,Sparql Endpoint},
  title = {{Utilisation d'une ontologie comme source de donn{\'{e}}es pour r{\'{e}}pondre {\`{a}} des questions cliniques}},
  year = {2010}
  }

• R. Choquet, S. Qouiyd, E. Pasche, C. Daniel, O. Boussaïd, and M. Jaulent, « Un modèle de connaissances pour mesurer la qualité d’une source d’information, » in Ingénierie de la connaissance (ic2010), 2010.
  [Bibtex]

  @inproceedings{70,
  abstract = {La multiplication des bases de donn{\'{e}}es pose dans de nombreux domaines la question du caract{\`{e}}re informationnel des donn{\'{e}}es et de la connaissance qu'elles peuvent g{\'{e}}n{\'{e}}rer. Les standards et autres ressources s{\'{e}}mantiques permettent d'apporter un cadre d'interpr{\'{e}}tation aux donn{\'{e}}es. L'alignement des donn{\'{e}}es {\`{a}} ces ressources reste cependant difficile. Nous proposons un mod{\`{e}}le de qualit{\'{e}} de l'information permettant de mesurer et d'am{\'{e}}liorer le contenu informationnel de donn{\'{e}}es de sant{\'{e}}. Nous exp{\'{e}}rimentons ce mod{\`{e}}le sur des donn{\'{e}}es r{\'{e}}elles dans le cadre d'un projet europ{\'{e}}en DebugIT1 o{\{}{\`{u}}{\}} les donn{\'{e}}es sont partag{\'{e}}es afin de g{\'{e}}n{\'{e}}rer de nouvelles connaissances dans le domaine de l'antibior{\'{e}}sistance.},
  author = {Choquet, Remy and Qouiyd, Samiha and Pasche, Emilie and Daniel, Christel and Boussa{\"{i}}d, Omar and Jaulent, Marie-Christine},
  booktitle = {Ing{\'{e}}nierie de la Connaissance (IC2010)},
  keywords = {Entrep{\{}{\^{o}}{\}}ts de donn{\'{e}}es,Informatique M{\'{e}}dicale. Repr{\'{e}}sentation des connais,Qualit{\'{e}} de l'information},
  title = {{Un mod{\`{e}}le de connaissances pour mesurer la qualit{\'{e}} d'une source d'information}},
  year = {2010}
  }

• D. Schober, M. Boeker, J. Bullenkamp, C. Huszka, K. Depraetere, D. Teodoro, N. Nadah, R. Choquet, C. Daniel, and S. Schulz, « The DebugIT core ontology: semantic integration of antibiotics resistance patterns., » Studies in health technology and informatics, vol. 160, p. 1060–1064, 2010.
  [Bibtex]

  @article{66,
  abstract = {Antibiotics resistance development poses a significant problem in today{\{}$\backslash$textquoteright{\}}s hospital care. Massive amounts of clinical data are being collected and stored in proprietary and unconnected systems in heterogeneous format. The DebugIT EU project promises to make this data geographically and semantically interoperable for case-based knowledge analysis approaches aiming at the discovery of patterns that help to align antibiotics treatment schemes. The semantic glue for this endeavor is DCO, an application ontology that enables data miners to query distributed clinical information systems in a semantically rich and content driven manner. DCO will hence serve as the core component of the interoperability platform for the DebugIT project. Here we present DCO and an approach thet uses the semantic web query language SPARQL to bind and ontologically query hospital database content using DCO and information model mediators. We provide a query example that indicates that ontological querying over heterogeneous information models is feasible via SPARQL construct- and resource mapping queries.},
  author = {Schober, Daniel and Boeker, Martin and Bullenkamp, Jessica and Huszka, Csaba and Depraetere, Kristof and Teodoro, Douglas and Nadah, Nadia and Choquet, Remy and Daniel, Christel and Schulz, Stefan},
  issn = {0926-9630},
  journal = {Studies in health technology and informatics},
  keywords = {Databases,Drug Resistance,Factual,Information Storage and Retrieval,Internet,Microbial,Semantics,Software},
  pages = {1060--1064},
  title = {{The DebugIT core ontology: semantic integration of antibiotics resistance patterns.}},
  volume = {160},
  year = {2010}
  }

• D. Ouagne, N. Nadah, D. Schober, R. Choquet, D. Teodoro, D. Colaert, S. Schulz, M. Jaulent, and C. Daniel, « Ensuring HL7-based information model requirements within an ontology framework., » Studies in health technology and informatics, vol. 160, p. 912–916, 2010.
  [Bibtex]

  @article{67,
  abstract = {This paper describes the building of an HL7-based Information Model Ontology (IMO) that can be exploited by a domain ontology in order to distribute querying over different clinical data repositories. We employed the Open Medical Development Framework (OMDF) based on a model driven development methodology. OMDF provides model transformation features to build an HL7-based information model that covers the conceptual scope of a target project. The resulting IMO is used to mediate between ontologically queries and information retrieval from semantically less defined Hospital Information Systems (HIS). In the context of the DebugIT project - which scope corresponds to the control of infectious diseases and antimicrobial resistances - Information Model Ontology is integrated to the DebugIT domain ontology in order to express queries.},
  author = {Ouagne, David and Nadah, Nadia and Schober, Daniel and Choquet, R{\'{e}}my and Teodoro, Douglas and Colaert, Dirk and Schulz, Stefan and Jaulent, Marie-Christine and Daniel, Christel},
  issn = {0926-9630},
  journal = {Studies in health technology and informatics},
  keywords = {Communicable Disease Control,Drug Resistance,Health Level Seven,Hospital Information Systems,Microbial,Systems Integration},
  pages = {912--916},
  title = {{Ensuring HL7-based information model requirements within an ontology framework.}},
  volume = {160},
  year = {2010}
  }

• R. Choquet, S. Qouiyd, D. Ouagne, E. Pasche, C. Daniel, O. Boussaïd, and M. Jaulent, « The Information Quality Triangle: a methodology to assess clinical information quality., » Studies in health technology and informatics, vol. 160, p. 699–703, 2010.
  [Bibtex]

  @article{68,
  abstract = {Building qualitative clinical decision support or monitoring based on information stored in clinical information (or EHR) systems cannot be done without assessing and controlling information quality. Numerous works have introduced methods and measures to qualify and enhance data, information models and terminologies quality. This paper introduces an approach based on an Information Quality Triangle that aims at providing a generic framework to help in characterizing quality measures and methods in the context of the integration of EHR data in a clinical datawarehouse. We have successfully experimented the proposed approach at the HEGP hospital in France, as part of the DebugIT EU FP7 project.},
  author = {Choquet, R{\'{e}}my and Qouiyd, Samiha and Ouagne, David and Pasche, Emilie and Daniel, Christel and Boussa{\"{i}}d, Omar and Jaulent, Marie-Christine},
  issn = {0926-9630},
  journal = {Studies in health technology and informatics},
  keywords = {Clinical,Decision Support Systems,Delivery of Health Care,Electronic Health Records,France,Health Care,Models,Organizational,Quality Assurance},
  pages = {699--703},
  title = {{The Information Quality Triangle: a methodology to assess clinical information quality.}},
  volume = {160},
  year = {2010}
  }

• R. Choquet, D. Teodoro, G. Mels, and A. Assele, « Partage de données biomédicales sur le web sémantique, » in Ic2010, 2010.
  [Bibtex]

  @inproceedings{69,
  abstract = {L{\{}$\backslash$textquoteright{\}}explosion de la quantit{\{}{\'{e}}{\}} de donn{\{}{\'{e}}{\}}es {\{}{\`{a}}{\}} traiter et {\{}{\`{a}}{\}} partager, particuli{\{}{\`{e}}{\}}rement dans le domaine biom{\{}{\'{e}}{\}}dical, pousse la communaut{\{}{\'{e}}{\}} {\{}{\`{a}}{\}} construire des syst{\{}{\`{e}}{\}}mes int{\{}{\'{e}}{\}}gr{\{}{\'{e}}{\}}s o{\{}{\`{u}}{\}} s{\{}{\'{e}}{\}}mantique et donn{\{}{\'{e}}{\}}es sont coupl{\{}{\'{e}}{\}}es. Le projet Europ{\{}{\'{e}}{\}}en DebugIT adopte les technologies du web s{\{}{\'{e}}{\}}mantique pour partager des donn{\{}{\'{e}}{\}}es li{\{}{\'{e}}{\}}es {\{}{\`{a}}{\}} l{\{}$\backslash$textquoteright{\}}{\{}{\'{e}}{\}}mergence de la r{\{}{\'{e}}{\}}sistance aux antibiotiques en Europe. Nous proposons une mise en pratique de ces technologies {\{}{\`{a}}{\}} travers un cadre d{\{}$\backslash$textquoteright{\}}interop{\{}{\'{e}}{\}}rabilit{\{}{\'{e}}{\}} technique, syntaxique et s{\{}{\'{e}}{\}}mantique. Nous validerons l{\{}$\backslash$textquoteright{\}}approche sur des donn{\{}{\'{e}}{\}}es r{\{}{\'{e}}{\}}elles, multilingues et multi terminologiques.},
  author = {Choquet, Remy and Teodoro, Douglas and Mels, Giovanni and Assele, Ariane},
  booktitle = {IC2010},
  keywords = {Int{\{}{\'{e}}{\}}gration de donn{\{}{\'{e}}{\}}es,interop{\{}{\'{e}}{\}}rabilit{\{}{\'{e}}{\}} s{\{}{\'{e}}{\}}mantique,web s{\{}{\'{e}}{\}}mantique},
  title = {{Partage de donn{\'{e}}es biom{\'{e}}dicales sur le web s{\'{e}}mantique}},
  url = {http://ceur-ws.org/Vol-600/paper1.pdf},
  year = {2010}
  }

• R. Choquet, O. Boussaid, and M. C. Jaulent, « Mise en oeuvre d’une architecture d’aide à la décision en santé: le cas de l’HEGP, » , p. 1{\{}$\backslash$textendash{\}}1, 2009.
  [Bibtex]

  @article{Choquet:2009p5446,
  abstract = {Contexte:Int{\'{e}}gration et Entreposage de Donn{\'{e}}es de Sant{\'{e}} {\`{a}} l'H{\{}{\^{o}}{\}}pital Europ{\'{e}}en Georges Pompidou (Paris) {\`{a}} des fins d'analyse d{\'{e}}cisionnelle But: Faire un inventaire des donn{\'{e}}es utiles dans le SI de l'h{\{}{\^{o}}{\}}pital, proposer une mod{\'{e}}lisation commune et int{\'{e}}gr{\'{e}}e, relier ces donn{\'{e}}es {\`{a}} leur sens dans les terminologies propos{\'{e}}es dans la litt{\'{e}}rature et proposer des outils de navigation permettant d'avoir une vue unique int{\'{e}}gr{\'{e}}e des donn{\'{e}}es relatives au patient Nature des donn{\'{e}}es: Donn{\'{e}}es cliniques, biologie (antibiogrammes), prescription (antibioth{\'{e}}rapie)Verrous scientifiques: Int{\'{e}}gration de donn{\'{e}}es op{\'{e}}rationnelles ayant des types diff{\'{e}}rents, des sens diff{\'{e}}rents, ainsi que des niveaux de granularit{\'{e}} diff{\'{e}}rents; dans un contexte d{\'{e}}cisionnelTh{\`{e}}matique de recherche: Datawarehouse (Entrep{\{}{\^{o}}{\}}t de donn{\'{e}}es) et OLAPApproche retenue: Reconsid{\'{e}}rer la mod{\'{e}}lisation multidimensionnelle utilis{\'{e}}e pour mod{\'{e}}liser les entrep{\{}{\^{o}}{\}}ts de donn{\'{e}}es en utilisant une m{\'{e}}thode conceptuelle et logique innovante: le mod{\`{e}}le associatif.},
  author = {Choquet, R and Boussaid, O and Jaulent, M C},
  month = {oct},
  pages = {1{\{}$\backslash$textendash{\}}1},
  title = {{Mise en oeuvre d'une architecture d'aide {\`{a}} la d{\'{e}}cision en sant{\'{e}}: le cas de l'HEGP}},
  url = {http://www.remychoquet.fr/pro/docs/Choquet-StMalo09.pdf},
  year = {2009}
  }

• R. Choquet, D. Kalra, and M. C. Jaulent, « Specification of an Inter-Operability Platform for the integration and exploitation of distributed clinical data, » American medical informatics association annual conference, p. 1{\{}$\backslash$textendash{\}}1, 2009.
  [Bibtex]

  @article{Choquet:2009p5447,
  abstract = {Clinical Information Systems (CIS) manage data that are heterogeneous and do not always follow standard semantic reference. An Inter-Operability Platform (IOP) addresses the key issue of establishing semantic interoperability between the real world (the CIS) and various components that have to exploit the real world data. We present the functional and architectural specification architecture of such IOP system. This work has been done within the context of the DebugIT1 European project (FP72).},
  author = {Choquet, R and Kalra, D and Jaulent, M C},
  journal = {American Medical Informatics Association Annual Conference},
  month = {mar},
  pages = {1{\{}$\backslash$textendash{\}}1},
  title = {{Specification of an Inter-Operability Platform for the integration and exploitation of distributed clinical data}},
  year = {2009}
  }

• D. Teodoro, E. Pasche, R. Wipfli, J. Gobeill, R. Choquet, C. Daniel, P. Ruch, and C. Lovis, « Integration of biomedical data using federated databases, » Proceedings of the 22th conference of swiss medical informatics, p. 1{\{}$\backslash$textendash{\}}5, 2009.
  [Bibtex]

  @article{Teodoro:2009p5442,
  abstract = {The expansion of biomedical knowledge, reduction in computing costs and spread of IT facilities have conducted to an escalation of the biomedical electronic data. However, these data are rarely integrated and analysed because of the insufficiency of specialised tools. This paper presents a pilot system that will be used in the European FP7 DebugIT project to integrate biomedical data from several healthcare centres across Europe. The system aims at solving complex problems derived from the technical and semantic heterogeneity intrinsic to these kinds of data sources as well as from the absence of reliability of the distributed system.},
  author = {Teodoro, D and Pasche, E and Wipfli, R and Gobeill, J and Choquet, R and Daniel, C and Ruch, P and Lovis, C},
  journal = {Proceedings of the 22th conference of swiss medical informatics},
  month = {sep},
  pages = {1{\{}$\backslash$textendash{\}}5},
  title = {{Integration of biomedical data using federated databases}},
  url = {http://www.remychoquet.fr/pro/docs/SSIM09teodoro.pdf},
  year = {2009}
  }

• D. Teodoro, R. Choquet, and E. Pasche, « Biomedical data management: a proposal framework, » Stud health technol \ldots, p. 175–179, 2009.
  [Bibtex]

  @article{Teodoro2009,
  author = {Teodoro, Douglas and Choquet, R{\'{e}}my and Pasche, Emilie},
  doi = {10.3233/978-1-60750-044-5-175},
  file = {:Users/choquetr/Library/Application Support/Mendeley Desktop/Downloaded/Teodoro, Choquet, Pasche - 2009 - Biomedical data management a proposal framework.pdf:pdf},
  isbn = {9781607500445},
  journal = {Stud Health Technol {\ldots}},
  keywords = {data integration,federated databases,view integration},
  pages = {175--179},
  title = {{Biomedical data management: a proposal framework}},
  url = {http://remychoquet.fr/pro/docs/mie09teodoro.pdf},
  year = {2009}
  }

• R. Choquet, C. Daniel, O. Boussaid, and M. C. Jaulent, « Etude méthodologique comparative de solutions d’entreposage de données de santé à des fins décisionnelles, » 9ème conference internationale sur la science des systemes de sante, p. 1{\{}$\backslash$textendash{\}}6, 2008.
  [Bibtex]

  @article{Choquet:2008p5440,
  abstract = {Warehousing medical data with healthcare analysis goals introduces several issues. Knowledge representation in constant evolution implies the need to find new technological approaches, which are still being researched. We propose in this article, to compare several technologies in development, in order to define specific methodological approaches for warehousing medical data.},
  author = {Choquet, R and Daniel, C and Boussaid, O and Jaulent, M C},
  journal = {9{\`{e}}me CONFERENCE INTERNATIONALE SUR LA SCIENCE DES SYSTEMES DE SANTE},
  pages = {1{\{}$\backslash$textendash{\}}6},
  title = {{Etude m{\'{e}}thodologique comparative de solutions d'entreposage de donn{\'{e}}es de sant{\'{e}} {\`{a}} des fins d{\'{e}}cisionnelles}},
  url = {http://www.remychoquet.fr/pro/docs/ICSSHC08choquet.pdf},
  year = {2008}
  }

• O. Boussaid, R. B. Messaoud, R. Choquet, and S. Anthoard, X-warehousing: An XML-based approach for warehousing complex data, , 2006, vol. 4152 LNCS.
  [Bibtex]

  @book{Boussaid2006a,
  abstract = {XML is suitable for structuring complex data coming from different sources and supported by heterogeneous formats. It allows a flexible formalism capable to represent and store different types of data. Therefore, the importance of integrating XML documents in data warehouses is becoming increasingly high. In this paper, we propose an XML-based methodology, named X-Warehousing, which designs warehouses at a logical level, and populates them with XML documents at a physical level. Our approach is mainly oriented to users analysis objectives expressed according to an XML Schema and merged with XML data sources. The resulted XML Schema represents the logical model of a data warehouse. Whereas, XML documents validated against the analysis objectives populate the physical model of the data warehouse, called the XML cube. {\textcopyright} Springer-Verlag Berlin Heidelberg 2006.},
  author = {Boussaid, O. and Messaoud, R.B. and Choquet, R. and Anthoard, S.},
  booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
  isbn = {3540378995},
  issn = {16113349},
  title = {{X-warehousing: An XML-based approach for warehousing complex data}},
  volume = {4152 LNCS},
  year = {2006}
  }

• O. Boussaid, R. B. Messaoud, R. Choquet, S. Anthoard, and E. Laboratoire, « Conception et construction d’entrep\ô\ts en XML, » La rnti correnspondant à la 2ième journée francophone sur les entrep\ô\ts de données et l’analyse en ligne eda’06 versaille 19 juin 2006, 2006.
  [Bibtex]

  @article{Boussaid:2006p1340,
  abstract = {Les entreprises sont de plus en plus concern{\'{e}}es par des donn{\'{e}}es dites complexes, se pr{\'{e}}sentant sous une forme autre que num{\'{e}}rique ou symbolique, issues de sources diff{\'{e}}rentes et ayant des formats h{\'{e}}t{\'{e}}rog{\`{e}}nes. Pour une exploi- tation {\`{a}} des fins d{\'{e}}cisionnelles, ces donn{\'{e}}es complexes n{\'{e}}cessitent un travail pr{\'{e}}paratoire pour les structurer et les homog{\'{e}}n{\'{e}}iser.La prolif{\'{e}}ration des donn{\'{e}}es sous forme de documents XML incite {\`{a}} une so- lution d'entreposage. Nous proposons dans ce papier une approche bas{\'{e}}e sur XML, d'entreposage de donn{\'{e}}es complexes contenues dans des documents XML, appel{\'{e}}e X-Warehousing. Celle-ci d{\'{e}}finit une m{\'{e}}thodologie pour concevoir des entrep{\{}{\^{o}}{\}}ts de donn{\'{e}}es complexes {\`{a}} l'aide du formalisme XML. Pour valider notre approche, nous avons impl{\'{e}}ment{\'{e}} une application Java et nous avons r{\'{e}}alis{\'{e}} une {\'{e}}tude de cas sur des donn{\'{e}}es complexes concernant les r{\'{e}}gions suspectes sur des mammographies.},
  author = {Boussaid, O and Messaoud, R B and Choquet, R and Anthoard, S and Laboratoire, E},
  journal = {la RNTI correnspondant {\`{a}} la 2i{\`{e}}me journ{\'{e}}e francophone sur les entrep{\{}{\^{o}}{\}}ts de donn{\'{e}}es et l'analyse en ligne EDA'06 Versaille 19 juin 2006},
  title = {{Conception et construction d'entrep{\{}{\^{o}}{\}}ts en XML}},
  year = {2006}
  }

• O. Boussaid and R. Messaoud, « X-warehousing: an xml-based approach for warehousing complex data, » Advances in databases \ldots, 2006.
  [Bibtex]

  @article{Boussaid2006,
  author = {Boussaid, Omar and Messaoud, R},
  file = {:Users/choquetr/Library/Application Support/Mendeley Desktop/Downloaded/Boussaid, Messaoud - 2006 - X-warehousing an xml-based approach for warehousing complex data.pdf:pdf},
  journal = {Advances in Databases {\ldots}},
  title = {{X-warehousing: an xml-based approach for warehousing complex data}},
  url = {http://www.springerlink.com/index/63485854MU38U4H2.pdf},
  year = {2006}
  }