From BIOINFOMED to INFOBIOMED
Facing the traditionally strong North-American research centres and the growing importance of Asia it is obvious that there are no national solutions for Europe to persist in scientific competition. However, research culture throughout Europe has evolved differently from both a mental and political point of view. By Michael Wenzel
Since 1984 the EC has been conducting several framework programmes to enhance research and technological development within its borders. Currently the sixth framework programme is in force and will - after a four-year run - cease at the end of this year. The aim is to build up the European Research Area (ERA), a structure to improve greater cooperation between economic and social as well as scientific institutions to promote excellence, competitiveness and innovation. The total budget is EUR 17.5 billion, divided into EUR 16.270 billion for the European Community (EC) and EUR 1.230 billion for Euratom. To further the programmes aims, two new instruments were introduced: networks of excellence (NoEs) and integrated projects. While integrated projects encourage research activities focusing on clearly defined scientific and technological objectives and possibly the establishment of a marketable product, NoEs display a higher academic orientation. Here, multiple partners collaborate on a specific topic integrating their research activities and likewise expanding knowledge.
In April 2003, the participants of the EC-funded BIOINFOMED Study presented a so-called white paper, with a proposal for Community action. More than 30 experts concluded that a high potential of synergy exists between the separately evolved and established disciplines Bioinformatics (BI) and Medical Informatics (MI). Taking into account the growing knowledge of the human genome and progress in post-genomic research technologies, a benefit for public health (e. g. promotion of personalised healthcare) and for the improvement of competitiveness of European biotechnology can only be achieved by bridging the gap between the two disciplines towards the emerging field of Biomedical Informatics (BMI). Based on this report the EC made various calls of which one was answered by a group of BIOINFOMED participants and further academic and non-academic institutions, who applied as the INFOBIOMED NoE. Since January 2004, the 18 partners from 10 nations have been working together as an approved NoE coordinated by the Fundació Institut Municipal d'Investigació Mèdica (FIMIM) based in Barcelona, with clearly stated objectives.
Innovative approaches to complex diseases
Common diseases like cardiovascular disorders and cancer as well as infectious diseases produce a constant loss in terms of financial and human costs on health care systems and society in general. In addition to a high incidence, their outstanding complexity represents an obstacle to effective research. Therefore, they are priority targets of current biomedical approaches and a challenge for INFOBIOMED to face. There are four pilot projects concentrating on the application of BMI to current problems in selected fields.
The participating scientists are assessing the benefit of integrating pathway biology with host and pathogen genomics into the understanding and treatment of infectious disease, especially the interplay of the host interferon pathway with relevant viral pathogens. They develop novel tools supporting the integration of clinical and genetic data, disease reclassification, decision making and risk profiling of patients with periodontitis as a model for chronic inflammation, which is a contributory factor to a wide range of common disorders like Alzheimer´s Disease and atherosclerosis. The progress of the concerted work is presented and discussed regularly on meetings of the participants with status updates being reported to the EC.
In developed countries, colon cancer represents one of the most frequent malignancies affecting women and men alike. It can occur in both sporadic and hereditary forms. Here, the most common type of hereditary colon cancer is HNPCC (Hereditary Non-Polyposis Colon Cancer), a malignancy of high penetration. Being predisposed by a defect in genes responsible for DNA repair, patients have an estimated 80 percent chance of being confronted with the diagnosis of colon cancer and other malignancies during their lifetime. In order to obtain the knowledge needed for the planning and organization of screening high-risk families, specialized registries are playing a keyrole. Since 1991 the HNPCC registry based in Hvidore/Denmark has collected epidemiological and molecular-genetic information from all Danish HNPCC-families in a database system and a corresponding pedigree-program. Data is collected by over 70 institutions, encompassing genetic as well as surgical departments. As different sets of data are collected and saved in various systems, interoperability between the different centres proves to be difficult. "The aim of our pilot", says Danish surgeon Inge Bernstein, "is developing a tool to exchange data on families with increased risk of CRC - HNPCC-families electronically in order to facilitate establishment of screening." In a concerted action with European experts, a workable standard of collected data was established. With the vast amount of data physicians and researchers have to face, issues like privacy and confidentiality grow in importance. Here it is necessary to establish structures that enable life science professionals to work with case-sensitive data derived from patient records for research and healthcare purposes. In the context of this pilot, the Danish Centre for Health Telematics established a system enabling departments to take advantage of a web-based data entry, which will launch in April. As a long-lasting structure derived from this project, Bernstein can already envision a physical tool developed for electronic data exchange on oncogenetic diseases, which will be available to the European community in an open source.
The obstacles Bernstein encounters are well known in the context of other pilots. "There is a fundamental problem in the way we manage information linking underlying biology to the patient phenotype and patient care will continue to be sub optimal until we solve it", states Scott Boyer, senior research scientist at AstraZeneca in Sweden. He is concerned with the integration of BI and MI with special application to problems relevant to the pharmaceutical industry, especially the process of drug discovery. One of these problems is the complex regional pain syndrome (CRPS), a neuropathic disorder, the nature of which is characterised by pain and sensory-motoric disturbances. Yet the pathogenetical mechanisms of CRPS and suitable treatment are unclear. As multiple factors may play a role in the pathogenesis, an interdisciplinary approach seems to be appropriate. "We can try completely different approaches to problems we have traditionally struggled with", Dr. Boyer characterizes the advantages of working in an international network. "Fresh ideas from outside the pharmaceutical industry are the best way to improve the way we work inside." For example, the pharmacists are supported by Dutch experts in semantics from the university of Amsterdam, who identify known molecular pathways involved in CRPS by literature mining.
Training for the future
INFOBIOMED is not limited to the participants. As a service for the whole scientific community, the project offers collaborative tools to be downloaded freely from its website in order to support discussion and data sharing among researchers. One example is LINK3D, an innovative software that allows users to share files with three-dimensional structures of different formats and to directly interact on the file in real-time. Another activity unique to NoEs is the issue of training and mobility. Here, INFOBIOMED offers a web-based inventory of training opportunities for postgraduates and an own brokerage service for jobs on the European level. This enables scientists to practically update their knowledge in the field of BMI at centres of excellence. As a side effect it is expected that the knowledge transfer complements organizations and promotes research infrastructure.
In order to continue promoting the international dialogue between disciplines in the future, INFOBIOMED arranged a special event. From 12th to 16th of September 2005, two groups of five students from different European institutions and backgrounds were invited to a hotel in Viladrau near Barcelona to work together on a case study that would benefit from an integrative approach. Their assignment was not only to be able to present a solution or at least a course of action to the presented problem at the end of the week but they were also supposed to present what they had learned with regards to working with people from disciplines other than their own - even crossing language barriers. Kristina Hettne, a 28 years old bioinformatician working as a scientist for AstraZeneca, worked as a facilitator. "The students were very enthusiastic and eager to perform their best", she remembers. "They worked very hard and they also experienced the ups and downs of working in a multi-disciplinary environment." Though the participants received new input on ways to approach scientific problems, there was also the frustrating insight that a vast body of knowledge exists outside the scope of the personally chosen discipline. "Many found out that it can be very beneficial for the group's success to force yourself to listen, compromise and try to fit the different pieces of knowledge together to a whole", Hettne resumes the experiences made by the young scientists and which are certainly not unknown to fully-fledged INFOBIOMED partners. "Everybody is forced to broaden their views, respect how different disciplines view the same issue and combine their own national perspectives with a greater ambition", says the project´s manager, Carlos Diaz. "It really helps to build a common notion of what Europe is."
For further information on the INFOBIOMED NoE please visit the website
http://www.infobiomed.org
