European Network of Excellence (NoE) in Biomedical Informatics, to facilitate ..... Journal of the American Medical Informatics Association 2003 NovâDec; 10 (6):.
The INFOBIOMED Network of Excellence: Facilitating Training and Mobility in Biomedical Informatics in Europe Guillermo de la Calle, Victor Maojo, Mario Benito Biomedical Informatics Group, Artificial Intelligence Lab., Facultad de Informática, Universidad Politécnica de Madrid, Campus de Montegancedo s/n, 28660 Boadilla del Monte, Madrid, Spain {gcalle, vmaojo, mariobr}@infomed.dia.fi.upm.es
Abstract. In this paper we present the work carried out within INFOBIOMED, the European Network of Excellence (NoE) in Biomedical Informatics, to facilitate training and mobility in the area. An analysis of past experiences in both Medical Informatics and Bioinformatics has led to various actions. In this scenario, we have elaborated three actions: (1) a survey of the training and mobility situation, needs and actions to be taken, (2) a Biomedical Informatics course database (ICD), and (3) a Mobility Brokerage Service (MBS). We describe the use of Web Services to build the MBS, designed to facilitate the exchange of professionals within the consortium, belonging to ten European countries. The goal of INFOBIOMED is to expand these initiatives to other NoEs and institutions within the European Union. Keywords: Biomedical Informatics, Medical Informatics, Bioinformatics, Training, Mobility, Web Services
1. Introduction Over the last few years, many academic, industrial and institutional initiatives have launched a new area: Biomedical Informatics (BMI), at the intersection between Medical Informatics (MI) and Bioinformatics (BI). Traditionally these disciplines have evolved without interacting. As regards, it has been proposed [1] that MI could provide the methods, tools and lessons learned in more than forty years of experience in developing clinical applications. Meanwhile, BI could provide a scientific basis that could be quite important to advance scientific knowledge in areas such as physiology and the underlying pathological processes of diseases. In particular, the new concept of “Genomic Medicine” could benefit from a strong support and interaction with BMI. One of the most important constraints to advance towards molecular medicine and BMI is the shift in education that will be required for physicians to learn how to interpret and manage genomic and genetic information in their clinical routines. The knowledge and reasoning methods that will be needed in this new concept of medicine
may be partially provided by informatics tools. Physicians should learn how to use those tools but it does not sound reasonable to make them fully understand, for instance, how to interpret microarray results or SNPs (single nucleotide polymorphisms) information. A different issue will be how to create the methods and build the informatics tools that will be needed to facilitate the work of practitioners. For that purpose, different backgrounds and expertises will be needed. INFOBIOMED [2] is a European Network of Excellence (NoE) –funded by the European Commission (EC)– composed by organizations and universities from ten different countries. Its main objective is the establishment and strengthening of the BMI community at European level in order to support individualized healthcare. Four pilots focused on different problems have been established to demonstrate the benefits of this new approach. The training of new BMI experts is one of the most important challenges. For that reason, the INFOBIOMED mobility program is focused in promoting exchanges between organizations. In this paper we present some of the work that has been carried out over the last few years to enhance training and mobility in BMI. We present the Mobility Brokerage Service, developed at the UPM to enhance the publication of training and job opportunities (both offers and demands) over the Web. While these initiatives were originally internal to the INFOBIOMED NoE, they are being expanded to make them available to the whole BMI community.
2. Background Proposals for a stronger interaction between MI and BI professionals have been recently made. Collaborative efforts may be beneficial to exchange research results and methods as well as computing tools [3]. Some of the underlying issues below both disciplines have common points that could be shared and exchanged. This was the central focus of the BIOINFOMED study [4, 5], supported by the European Commission: to study synergies between BI and MI and elaborate a R&D agenda for the forthcoming programmes at the European Commission. Associations such as the American College of Medical Informatics are promoting efforts to analyze this issue. Different programs and initiatives have been developed over the last decades to support training in both areas. The rise of BMI introduces new challenges that have been addressed by US universities such as Stanford or Columbia, with BMI programs that integrate both MI and BI and an increasing number of institutions in Europe. Related approaches have been taken in Europe, such as at the Karolinska Institute in Sweden, where a PhD Program in medical bioinformatics has been launched. The purpose is “to build up competence in bioinformatics with special emphasis on biomedical and clinical applications”. In this sense, the European Commission has strongly supported the field and academic initiatives in BMI, since an early conference that took place in Brussels, December 2001, to support BMI. Within these initiatives, the various Network of Excellence funded by the e-health division, DG IST, have created their own strategies to support training in BMI. Another EC-funded initiative is the SYMBIOmatics project [6]. This project is funded by the Sixth European Framework Programme for Research and Technological Development. It is coordinated by the EBI (UK) and is composed by nine partners from six different European countries. The main objective is to summarize in a white paper the state-of-the-art in BMI in Europe. This information will provide the
appropriate input to future European scientific and funding policy. Some results of this study and the work done by the different e-health NoEs is expected, at the time of writing this paper, to be presented in a wide Open meeting in July 2006 in Brussels,
3. Methods Various initiatives to study and support training and mobility have been carried out within the members of the INFOBIOMED Consortium. These initiatives are three: a) a survey of training courses, infrastructures and actions needed in the field, at the European level, b) elaboration of a BMI course database, and c) a Web Service-based Mobility Brokerage Service (MBS), to facilitate exchange of students and professionals. This paper is focused on the MBS, which is presented below: 3.1. The Mobility Brokerage Service (MBS) A Web Service-based brokerage service was set up and implemented to integrate distributed information related to mobility. Previously, a survey was carried out to identify the main barriers to solve and the features that the MBS should include. Results from this survey were adopted in the system. The MBS includes Web Services technology and facilitates different kinds of queries and information retrieval. More details about the implementation and visual aspects are given in the next sections. After analyzing the information collected in the survey, some interesting results appeared. For almost 75% of participants, the main barrier to participate in mobility activities was the lack of funding. The lack of information about host offers and lack of time appeared as other important drawbacks. Based on these results, some practical solutions have been deployed to address these two principal drawbacks. To supply the lack of funding, a Mobility Funding System (MFM) has been approved by the Training and Mobility Committee (TMC) of INFOBIOMED. Basically MFM consists on offering economic incentives to foster exchanges between partner staffs. On the other hand, a Mobility Brokerage Service (MBS) has been implemented to deal with the lack of information about mobility offers. As pointed out above, another important barrier for the consolidation of BMI as a novel synergical discipline is the current lack of information about education possibilities. It might not be easy for researchers to find specific opportunities to learn and consolidate their expertise on this discipline. The mobility action plan intends to promote exchanges of experts among European institutions. Both host organizations and participants would be benefited with the exchanges. To facilitate mobility opportunities searches and communicate host organizations with candidates, a Mobility Brokerage Service (MBS) has been developed within the INFOBIOMED Consortium. The MBS has been envisaged as a secure web on-line marketplace to promote mobility opportunities. The MBS has been designed following a novel and incipient technology. Its system architecture is service-oriented [7] and based on XML and web services. 3.2. Web Services concepts Web Services (WS) is an emerging technology arisen to address the problem of exchanging information among existing and new applications over Internet. They are based on consolidated technologies such as HTTP and XML for transporting and
representing data, respectively. Numerous attempts for integrating distributed programs appeared during the last 30 years, such as Common Object Request Broker Architecture (CORBA), Distributed Component Object Model (DCOM), Remote Procedure Call (RPC), and Java Remote Method Invocation (RMI). Three new protocols have arisen related to Web Services: WSDL (Web Services Definition Language) [8] is a W3C specification, SOAP (Simple Object Access Protocol) [9], and UDDI (Universal Description, Discovery, and Integration) [10]. There exist several implementations of these specifications and protocols, as well as Web services toolkits developed by different companies and organizations. For inexperienced users, WS are more complicated to set up and deploy than classical systems, but they offer interesting advantages. For instance, WS are platformindependent, allowing interconnecting heterogeneous applications and systems without problems. WS can also be combined with other WS. 3.3. Implementation The MBS has being implemented as a web application. JavaServer Pages (JSPs) and Servlets are used to generate dynamically web pages with the information requested by users. The web server and the servlet container use Apache Jakarta Tomcat 5.0. This is an open and collaboratory environment. For storing data MySQL 4.0.20 has been selected. MySQL is the most popular open source DataBase Management System (DBMS), particularly suitable for developing web applications.
Figure 1. The INFOBIOMED Mobility Brokerage Service main page.
The internal functionalities are solved by using Web Services. We have defined several WS for different heterogeneous tasks (e.g., identification and validation of the users, managing candidates and hosts organizations information). We address traditional security issues such as identification, authentication, authorization, integrity and confidentiality of the data by using WS-Security. Security communications are addressed by using the Secure Socket Layer (SSL) protocol. The MBS is completely integrated and accessible through the INFOBIOMED official web site. Figure 1 shows a screenshot of the application. WS technology allows to store the databases in the same computer or access them over the Internet. For instance, a web application might be running at the official site server and each WS might be placed on different computers, remotely. Similarly, databases with the information about candidates and host organizations can be distributed. Access is transparent to users by using a common and uniform interface. The MBS allows users (candidates and host organizations) to register into the system, manage their own data, make suggestions and, finally, leave the application. Users can also look for offers or demands depending on their role. The system presents two significant functionalities for registered users: • •
Mobility opportunities and job offers can be searched using textual searching approaches or by graphically navigating the MBS by means of visual maps. Each time a position offer or demand is registered on the system, an automatic matching process is performed. When a match is found, an email is sent to the interested actors, inviting them to visit the site to review the information.
Since Web Services are based on HTTP and XML standards, no problems arise with proxies and firewalls. Communications are completely transparent in this sense. 3.4. The Matching System As exposed above, the matching system is a facility offered by the MBS to automatically find the opportunity or candidate wished. The keywords defined by the training topic thesaurus are used to improve the effectiveness and accuracy of the automatic searches. Keywords are classified in various main categories and subcategories. When a new offer or demand is introduced in the system, users are asked to indicate a set of keywords which define the area that fits better to their desires. Each time an offer is stored in the database, the matching process is automatically performed. The system tries to find matches between the new offer and the rest of existing demands. Additionally, searches are filtered using other criteria such as the kind of collaboration sought, the starting and ending dates or duration. Analogous situation happens when a demand is introduced. The system looks for the offers which satisfy the demand. Anytime a match is found, the user is notified by email. An email will invite each user to visit the MBS and check the news. The new matches are displayed using an animated icon.
4. Conclusions INFOBIOMED has addressed BMI education in the context of the European Union. Following a survey, a course database and a MBS were implemented to address these issues. This paper has shown some of its main features. WS technology provides different possibilities for integrating data sources. Within the NoE, four pilot applications are being developed, in the areas of pharmainformatics, genomic and microbiology, genomic and chronic inflammation, and genomic and colon cancer. Issues such as integration from different and heterogeneous data sources, common to all pilots, can be solved using similar approaches, such as service-oriented architectures. In the framework of INFOBIOMED, the Mobility Brokerage Service is the main approach used to promote mobility in the BMI. Also, it is expected that the others European e-health NoEs use the system developed for their own mobility programs.
Acknowledgments The present work has been funded by the European Commission (FP6, IST thematic area) through the INFOBIOMED NoE (IST-507585).
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