Simon Twigger @ MCW

I have put up a prototype of a simple PHP/MySQL Gene Ontology annotation tool. The tool is envisaged as a simple way to enter new GO annotations for a gene product and save those annotations in a database (MySQL). Our goal is to get away from Excel as an annotation tool and streamline the annotation entry, QC and submission process.

Basic QC for the annotations are performed to catch the typical data entry errors (invalid GO accession numbers) and checks are done against the latest GO terms (updated daily from GO) to prevent curators from entering newly obsolete terms.

New annotations are added into the single annotations table of the MySQL database and these are shown on the annotation form along with any existing gene annotations that have been submitted to the GO Consortium (obtained from the monthly GO db release). A configuration file is used to configure basic application properties such as: database connections, URLs to link to GO browsers and to database gene reports so the scripts can be easily configured to work in a different environment.

The prototype tool can be found here.