Four pilot applications will be developed by INFOBIOMED:

Pharmainformatics 
This pilot application will carry out research on the mutual impact of BMI and pharmaceutical research. Research in this area focuses on establishing an information continuum pathology – pathway – target – ligand. 
This pilot will be based in two case studies:

- Complex Regional Pain Syndrome (information continuum from pathology to ligand): all known pathways related to CRPS will be identified through literature mining. The known pathways will be associated or expanded (both obvious and non-obvious interactions will be investigated). Approved drugs or ligands that are active against members of the associated or expanded pathways will be identified with the help of compound/ligand databases. Finally it will be verified in original population database if the found approved drugs are being used, what their indications are, whether it is possible to use them in CRPS or whether patients on these drugs have an altered incidence of CRPS. 

- Nuclear Hormone Receptors (information continuum from ligand to pathology): relevant ligands and privileged structures as well as current PPARγ agonists will be identified. Using the target information from the previous step, all pathways related to the targets will be identified, and subsequently pathways will be differentiated or expanded. Individual members of the identified pathway will be linked to specific phenotypic information, i.e., phenotypes of genetic variants and deficiencies etc. It will be finally investigated whether any of the phenotypes identified from genetic variability are similar to the adverse effect patterns observed in PPARγ agonist patients. 

Genomics and microbiology 
The main activity objective is to inform and enhance clinical evaluation strategies through a comprehensive pathway-related understanding of the host/pathogen interaction. It aims to show the benefit of integrating pathway biology with host and pathogen genomics in the understanding and treatment of infectious disease. The study of the interferon signalling network and its interplay with clinically relevant pathogens such as Cytomegalovirus will serve as a model for the future development of intervention strategies.
Several tasks will be tackled in parallel:

i) Interferon pathway mapping and notational development;
ii) Pathway Database development;
iii) Protein interaction network analysis;
iv) The role of microRNA's in the host pathogen interaction;
v) The integration of new clinical data/ patient information and pathway related data and information.

Medical and Bioinformatics developmental work will be complemented by in vivo and in vitro based studies to confirm the validity of approaches developed in the course of this project.

Genomics and chronic inflammation 
Periodontitis has been chosen as a model to study complex chronic inflammatory diseases because of its multifactorial etiology (genetics, bacteria, and environment), relative high prevalence and broad and easy access to diseased patients' and normal tissues, genomic DNA, and access to the history of infections and other relevant data through the patient records. Structuring and integration of data streams constitutes the main challenge of this pilot. Existing data banks need integration, further genotyping support and a modern informatics approach for data analysis. This pilot will tackle the following tasks: 
i) finalization of a SOA report specific to this pilot; 
ii) mother database construction, including the selection of standard vocabulary, information retrieval and transformation and data incorporation; 
iii) development of an innovative tool for performing digital analysis of dental X-ray images; 
iv) privacy rules and confidentiality issues; 
v) genotyping database construction; 
vi) development of questionnaires to gather environmental data. 

Click here to download Internal Deliverable "State of the Art on Data Biomedical Informatics in Chronic Infectious and Inflammatory Disease Research: Periodontitis as a Case Study"

DIA Tool: is a Dental Image Analysis tool that applies an algorithm to extract tooth contours from most of the dental x-ray images and quantifies the amount of bone loss around the teeth. This system can be used as an auxiliary tool in the diagnosis of several pathologies, including periodontitis, and it can also be used to visualize the loss measurements (organized by date), to evaluate its evolution (disease history) and as an organizer of dental X-Ray images of the patients.

Genomics and colon cancer 
This pilot is based on the official Danish registry of HNPCC (Hereditary Non Polypose Colon Cancer) but its outreach aims at a European dimension and other oncogenetic diseases. The HNPCC-Register has registered from 1991 epidemiological and molecular-genetic information on all Danish HNPCC-families in a PARADOX-database system and a corresponding pedigree-program. The Register identifies HNPCC-families and recommended screening, as do the other genetic departments in Denmark and all the data are collected in the database. 
The aim of this pilot is to obtain knowledge useful for the planning and organization of screening in families with a high-risk of developing CRC. The tasks foreseen for this period will focus on: 

i) development of standards; 
ii) development of a web tools to transfer data; 
iii) conceptualization and development of a pedigree tool; 
iv) dealing with confidentiality issues; 
v) testing and evaluating the pilot version of the tools developed; 
vi) liase with and extend the pilot results to other countries and study its impact on other oncogenetic diseases.