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INFOGENMED: A virtual laboratory for accessing and integrating genetic and medical information for health applications

Objective

The main objective of the project is to build a virtual laboratory for accessing and integrating genetic and medical information for health applications, that we have denominated INFOGENMED. Users of the INFOGENMED project will be able to directly connect with remote medical and genetic databases, located at separate places. The user interface will be accessible using any standard Web browser, connected with a server of medical and genetic terms, based on Artificial Intelligence techniques. This server will provide user navigation and searching capabilities in multiple remote databases, in different languages. The information retrieved from remote databases will be stored for its integration with local health or clinical information. Results will be validated at different sites, involving health practitioners and patients.

Objectives:
- Determination of the needs of genetic and medical information in various pathologies, considered as "rare genetic diseases", in health environments;
- Design of the methods and development of tools for the integration of heterogeneous databases over Internet;
- Design and implementation of an interface to aid users to search, find and retrieve the contents of remote databases, based on a vocabulary server for the integration of medical and genetic terms and concepts;
- Development of an assistant to help health practitioners to use the designed methods and tools. Integration of the complete system and validation in the area of rare genetic diseases.

Work description:
During the last few decades, Medical Informatics (MI) professionals have built different systems for clinical and research purposes. Some examples are bibliographic databases such as MEDLINE, expert systems such as MYCIN or QMR, or unified vocabularies such as the UMLS. These systems have provided physicians with computing aids for patient care and management. The difficulties associated to the medical domain has given MI professionals a strong experience in solving the problems associated to medical practice and research. Meanwhile, Bioinformatics (BI) professionals have built large databases and solved different problems associated to the Human Genome Project. Little collaborative efforts have been carried out between MI and BI professionals to share efforts to solve the problems of both disciplines which are quite similar in some aspects.

This project is one of the first attempts to link MI and BI R&D by building methods and tools that can be reused in different medical and genetic domains and applications. The need to create new methods to integrate medical and genetic heterogeneous databases for genomic medicine was pointed out during a workshop held in Brussels last December to analyse the synergy between MI and BI. The INFOGENMED project is also linked to the BIOINFOMED study, funded by the Commission. This project we will build a system to integrate medical and genetic information from remote and heterogeneous sources over the Web. A navigation tool will allow users to find and select the kind of information they need. This information will be accessed, collected and unified by creating a virtual repository that will give users the impression that they are working with a real, physical database.

The following issues will be analysed:
1) integrated models of medical and genetic vocabularies;
2) unification approaches for heterogeneous databases, and;
3) pathway visualization using flowchart representation. Since the work is based on extended previous research successfully carried out by the consortium, no important risks are expected. The work will be evaluated in the domain of rare genetic diseases.

Milestones:
- Integration of clinical and genetic info from heterogeneous remote databases;
- Improving existing methods: Medical/Genetics virtual databases, Data warehouse, Distributed DBs;
- A vocabulary server that aims to combine existing terminology systems in Medicine and Genetics;
- Novel framework for clinicians to locate, search, access, retrieve and use genomic information in patient care(to be improved).

Funding Scheme

CSC - Cost-sharing contracts
Leaflet | Map data © OpenStreetMap contributors, Credit: EC-GISCO, © EuroGeographics for the administrative boundaries

Coordinator

UNIVERSIDADE DE AVEIRO
Address
Campo Universitario De Santiago
3800 Aveiro
Portugal

Participants (4)

INSTITUTO DE SALUD CARLOS III
Spain
Address
Calle Sinesio Delgado 4-6
28029 Madrid
LINKOEPINGS UNIVERSITET
Sweden
Address
Campus Valla
581 83 Linkoeping
STAB VIDA, INVESTIGACAO E SERVICOS EM CIENCIAS BIOLOGICAS LDA
Portugal
Address
Rua Dr. Carlos Manuel Saudade E Silva, Iote 8, 2? Esq.
2500 Caldas Da Rainha
UNIVERSIDAD POLITÉCNICA DE MADRID
Spain
Address
Avenida Ramiro De Maeztu 7
28040 Madrid