The EPIWORK project, funded by the EU under a FET Proactive Initiative in FP7, was multidisciplinary research effort aimed at developing the approriate framework of tools and knowledge needed for the design of epidemic forecast infrastructures. The XLDB Team is leading the development of the Epidemic Marketplace in EPIWORK.
In recent years a huge flow of quantitative social, demographic and behavioural data is becoming available spurring the quest for innovative technologies that can improve the traditional disease-surveillance systems, providing faster and better localized detection capabilities and resulting in a broad practical impact.
The research addressed most of the much needed development of modeling, computational and ICT tools, such as
- the foundation and development of the mathematical and computational methods needed to achieve prediction and predictability of disease spreading in complex social systems;
- the development of large scale, data driven computational models endowed with a high level of realism and aimed at epidemic scenario forecast;
- the design and implemention of original data-collection schemes motivated by identified modelling needs, such as the collection of real-time disease incidence, through innovative web and ICT applications.
- the set up of a computational platform for epidemic research and data sharing that will generate important synergies between research communities and countries.
- Fondazione Istituto per l‘Interscambio Scientifico, ISI, Italy (coordinator)
- Fundação Calouste Gulbenkian, FGC-IGC, Portugal
- Tel Aviv University, TAU, Israel
- Max Planck Gesellschaft zur Foerderung der Wissenschaften E.V., MPG, Germany
- Acquisto Inter BV, AIBV, The Netherlands
- London School of Hygiene and Topical Medicine, LSHTM, United Kingdom
- SMITTSKYDDS Institutet, SMI, Sweden
- Katholieke Universiteit Leuven, KULeuven, Belgium
- Bar Ilan University, BIU, Israel
- Fondazione Bruno Kessler, FBK, Italy
- Center for REsearch And CREATE-NET, Italy
- Telecommunication Experimentation for NETworked communities
- Faculty of Sciences University of Lisbon, FFCUL,Portugal
Seventh Framework Programme Theme (Information and Communication Technologies)
Grant agreement no 231807 for Large-scale Integrating Project
Duration: 48 months from 01 February 2009
The overall objective of an epidemic forecast infrastructure is ultimately the support of modeling approaches addressing the required complexity/realism requirements for explaining and predicting the spatio-temporal dynamics of infectious disease propagation at the global scale (with a focus on Europe). Here we develop an information platform to mediate access to distributed collections of public health data, offering an easy and safe way to share data for those data providers who want to collaborate with epidemiological modelers.
Researchers use this platform in multiple ways:
- as catalogue of data sources containing the metadata describing existing databases;
- as a forum to publish information about their own data, seeking modellers to collaborate with, and/or to seek sources of data that could be of interest to their epidemiological modelling efforts;
- as the host of mediating software that can automatically process queries for epidemiological data available from the information sources connected to the platform.
The project develoed a common meta-model for querying data of interest for epidemiological modelling architecture using semantic-web technologies. Moreover, the analysis of the collected datasets and their annotations and usage provides a rich environment for deriving an epidemiology ontology, which will help further on the integration and communication among the community of epidemiologists.
XLDB Research Team
The XLDB Team is leading the development of the Epidemic Marketplace in EPIWORK.
- Mário J. Silva
- Dulce Domingos (from GLOSS)
- Francisco Couto
- João Zamite
- João D Ferreira
- Paulo Graça
- Carlos Santos
- Tiago Posse
- Juliana Duque
- Fabrício Silva
- Hugo Ferreira
- Luís Filipe Lopes
- Patricia Sousa
- Hugo Santos
- Vera Carvalho
- Catia Pesquita
- Ana Paula Afonso
- Francisco M. Couto, Exploring the semantics of biomedical ontologies, Bioinformatics Open Days, Braga, March 2012 
- Francisco M. Couto, Untangling Biomedical Ontologies, Practical workshop: Bioinformatics and Systems Modelling, Faculty of Sciences, University of Lisbon, 2011
- Francisco M. Couto, Exploring the semantics of biomedical ontologies, in External Seminar at European Bioinformatics Institute, Hinxton, UK, 2011
- Mário J. Silva, Privacy in Socially Intelligent ICT. Imperial College, London, UK. ASSYST Perada Workshop - Towards a Science of Socially Intelligent ICT. August, 2010.
- Mário J. SIlva, The Epidemic Marketplace: An Information Platform for Epidemiological Data. Digital Epidemiology Wokhop, Turin, IT, 2013
Tiago Grego, Francisco Pinto, Francisco Couto, LASIGE: using Conditional Random Fields and ChEBI ontology.Proceedings of the International Workshop on Semantic Evaluation (SemEval2013) 2013.
Tiago Grego, Francisco Couto 2013: Enhancement of Chemical Entity Identification in Text Using Semantic Similarity Validation. PLOS ONE 5(8), e62984.
João Ferreira, Daniela Paolotti, Francisco Couto, Mário J. Silva 2012: On the usefulness of ontologies in epidemiologic research and practice. Journal of Epidemiology and Community Health.
Catia Pesquita, Francisco M. Couto 2012: Predicting the Extension of Biomedical Ontologies. PLOS Computational Biology 9(8), e1002630.
João D. Ferreira, Francisco M. Couto, Semantic Similarity in the Biomedical Domain. Braga, Portugal. Poster @ Bioinformatics Open Days 2012. 2012
Francisco M. Couto, João D. Ferreira, João Zamite, Carlos Santos, Tiago Posse, Paulo Graça, Dulce Domingos, Mário J. Silva, The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies.International Conference on Biomedical Ontologies (ICBO) 2012.
João D. Ferreira, Catia Pesquita, Francisco M. Couto, Mário J. Silva, Bringing epidemiology into the Semantic Web.International Conference on Biomedical Ontologies (ICBO) 2012.
Corrado Gioannini, João Zamite, Integrating the Gleamviz Simulator Tool with the Epidemic Marketplace Platform. Poster presented at EE2, Epiwork/Epifor 2nd International Workshop: Facing the Challenge of Infectious Diseases. 2012
João Zamite, Dulce Domingos, Mário J. Silva, Owner-Centred Group-Based Access Control for Epidemic Resources. Poster presented at EE2, Epiwork/Epifor 2nd International Workshop: Facing the Challenge of Infectious Diseases. 2012
João D. Ferreira, Francisco M. Couto, Mário J. Silva, Ontologies in the Epidemiological Domain. Poster presented at EE2, Epiwork/Epifor 2nd International Workshop: Facing the Challenge of Infectious Diseases. 2012
João D. Ferreira, Catia Pesquita, Francisco Couto, Mário J. Silva, Epiwork Deliverable 3.5: Epidemic Data Ontology Technical Report. Technical Report . University of Lisbon, Faculty of Sciences, LASIGE, January 2012.
Carla Patrícia Freitas Sousa, Epidemic Marketplace: Repositório e Web Services Master Thesis, University of Lisbon, Faculty of Sciences, January 2012.
Zamite, J., Silva, F., Couto, F., Silva, M. 2011: MEDCollector: Multisource epidemic data collector. Transactions on Large-scale Data-and Knowledge-centered Systems IV: Special Issue on Database Systems for Biomedical Applications (6990), 40--72.
Juliana Duque, Mediação Dados-Informação: Design de Informação para a Epidemic Marketplace Master Thesis, University of Lisbon, School of Fine Arts, November 2011.
Francisco Couto, Mário J. Silva 2011: Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology. Journal of Biomedical Semantics.
Catia Pesquita, Francisco Couto, Where GO is going and what it means for ontology extension.International Conference on Biomedical Ontologies 2011.
Bruno Tavares, Hugo Bastos, Daniel Faria, Joao D. Ferreira, Tiago Grego, Catia Pesquita, Francisco Couto, The Biomedical Ontology Applications (BOA) framework.Proceedings of ICBO 2011.
João D. Ferreira, Francisco Couto, Generic semantic relatedness measure for biomedical ontologies.Proceedings of ICBO 2011.
Hugo Ferreira, O Mediador do Epidemic Marketplace Master Thesis, University of Lisbon, Faculty of Sciences, February 2011.
Mário J. Silva, Francisco Couto, Dulce Domingos, Juliana Duque, Hugo Ferreira, Luís F. Lopes, Daniela Paolotti, Fabrício Silva, Patrícia Sousa, João Zamite, D 3.3 Public Release of the Epidemic Marketplace Platform Technical Report. Technical Report . LASIGE, University of Lisbon, Faculty of Sciences, September 2010.
Luis Filipe Lopes, A Metadata Model for the Annotation of Epidemiological Data Master Thesis, University of Lisbon, Faculty of Sciences, September 2010.
João Zamite, Multisource Epidemic Data Collector Master Thesis, University of Lisbon, Faculty of Sciences, September 2010.
Fabrício A.B. Silva, Mário J. Silva, Francisco Couto 2010: Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis. ERCIM News 82(), 43-44. Special Theme: Computational Biology.
Luis Filipe Lopes, Fabrício A.B. Silva, Francisco Couto, João Zamite, Hugo Ferreira, Carla Sousa, Mário J. Silva, Epidemic Marketplace: An Information Management System for Epidemiological Data..Proceedings of the ITBAM - DEXA 2010 2010.
João Zamite, Fabrício A.B. Silva, Francisco Couto, Mário J. Silva, MEDCollector: Multisource Epidemic Data Collector.Proceedings of ITBAM'10 - 1st International Conference on Information Technology in Bio- and Medical Informatics - DEXA 2010 August, 2010.
Mário J. Silva, Fabrício A.B. Silva, Luís Filipe Lopes, Francisco Couto, Building a Digital Library for Epidemic Modelling.Proceedings of ICDL 2010 - The International Conference on Digital Libraries 1, p. 447--459, New Delhi, India, 23--27 February, 2010. TERI Press -- New Delhi, India. Invited Paper.
Luis Filipe Lopes, João Zamite, Bruno Tavares, Francisco Couto, Fabrício A.B. Silva, Mário J. Silva, Automated Social Network Epidemic Data Collector.INForum - Simpósio de Informática September, 2009.