CE-12.04

Title: 

Distributed Apollo Annotations for ChadoDB

Author(s): 

Mani Brundha Kattamuri

Oral Defence Date: 

04/11/2012

Location: 

HH 301

Committee: 

Professors Murphy, Petkovic and C. Smith (Biology)

Abstract: 

In the genomic analysis community, researchers use annotation tools such as Apollo to manage gene models from the ChadoDB database. These researchers are often in different locations working remotely on the same instance of the database, which leads to communication delays. Further, when multiple users access the same instance of the database, it becomes difficult to review user annotations and undo any erroneous changes. This culminating experience project addresses these issues by allowing users to work on local instances of the database and then upload their annotations to a website for review by an Administrator user. This report describes the design, development, and evaluation of this Web application, which provides a mechanism for reviewing and uploading distributed genomic annotations. This application allows the user to upload their annotation files in GFF3 format and the administrator to review these annotations. Once reviewed, the annotations are propagated to the central database via a bulk loader script, which is invoked from the web application. The annotations made by a user to a local copy of the master database are converted from ChadoDB tuples to the GFF3 format using a Perl script. This script is based on a mapping algorithm that computes the GFF3 lines for a given annotation. The algorithm was developed by analyzing the state of the database before and after making the annotations to the corresponding GFF3 file formats. The developed Web application is fully functional and was tested for Web-browser and operating system compatibility along with functional testing. The code is being distributed as Open Source.

Keywords: 

Annotation, Apollo, ChadoDB, GFF3

Copyright: 

Mani Brundha Kattamuri