Disease-oriented research often includes mapping of genomic intervals that are associated or linked with a disease. This data is typically only accessible through the primary scientific literature. The Intrval system is a resource to store, manage, and retrieve genetic interval related information. The goal of this project is to develop a database to store interval information for diseases along with corresponding phenotype information. The system is Java-based and allows the scientific community to upload to and view data in the database.
The Intrval system is divided into three parts: IntrvalDB, Intrval, and IntrvalWeb.
IntrvalDB consists of a publicly accessible mysql database used to store and retrieve interval data. All data stored in the database is available to the public. Each interval is associated with one or more publications in PubMed, therefore every interval submission (submission methods are discussed in the Intrval and IntrvalWeb sections) must include at least one PubMed id for the corresponding publication(s). Accepted submissions are given accessions starting with INT followed by six digits (ex. INT000001). Each interval is associated with a particular disease and is defined by flanking genetic markers. If an interval was defined by something other than markers it is acceptable to find the two closest markers and specify +/- offsets to get the desired location.
The database is located at public.eng.uiowa.edu on the default mysql port (3306). The database name is "intrval" and can be accessed with the username "anonymous" which does not require a password.
Intrval is a Java application which is deployed using Java Web Start technology. Intrval provides a graphical user friendly interface to access data in IntrvalDB. Intervals are drawn alongside corresponding chromosomes. Using the Ensembl database Intrval provides a list of all genes which are located in any intervals that are selected. Intrval also allows users to load sets of genes which can be used as inputs to a scoring algorithm which returns a list of ranked candidate genes (This is discussed further in the scoring section).
Users can load their own private intervals to be displayed without submitting them for integration into the database. These intervals are stored on the users file system. This allows users to take advantage of the benefits of Intrval when working on current research without giving their data to the public. Then after publishing the user can easily submit their now public intervals.
IntrvalWeb consists of a series of JSPs which allow the user to view data in the database. Its purpose is to provide quick and easy access to the interval data without having to lauch a bulky Java application.