Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology - Biomedical Engineering Systems and Technologies - page 382

In order to start using this framework we needed to have preinstalled a MySQL
server to store its database, an Apache Tomcat web server for deploying web services
and a simple user interface, and the Java Development Kit for generation of SQL and
HTML code.

Fig. 2. Oralome architecture

Along with the Oralome application, we developed tools and wrappers to obtain
specific information on each of the elements that build up the system (proteins, dis-
eases, pathways and others). For this, we carried out a first survey of sources where
this information would be available, and built a runnable script to update the Oralome
database.
This data fetch is made easier using Molgenis. It bundles a Database API that has
the advantage of hiding complex SQL commands.
To import and filter the information needed in our database, we used Java as the
programming language because it is highly compatible with most APIs provided by
the major external services resources (UniProt, KEGG, and NCBI Entrez Utilities).

3.4 Oralcard Development

In order to take advantage of the Oralome functionalities, we propose a tool that
enables searching over the oral cavity database and show different and customized
views for each entity. This led to the OralCard web application, a fundamental