We introduce an interactive visualization called ADVISe, which tackles the problem of visualizing evolutions in enzyme annotations across several releases of the UniProt/SwissProt database. More specifically, we visualize the dynamics of Enzyme Commission numbers (EC numbers), which are a numerical and hierarchical classification scheme for enzymes based on the chemical reactions they catalyze.
An EC number consists of four numbers separated by periods and represents a progressively finer classification of the catalyzed reaction. The proposed interactive visualization gives a macro view of the changes and presents further details on demand, such as frequencies of change types segmented by levels of generalization and specialization as well as by enzyme families. Users can also explore entry metadata.
With this tool, we were able to identify trends of specialization, database growth and exceptions in which EC numbers were deleted, divided or created and revisions of past annotation errors.
There is a pre-packed virtual machine that you can import into VirtualBox. It comes with the project's full database and the application itself, that is launched when the OS boots.
ADVISe uses data stored in a MySQL database. Please set up your environment according to the instructions present in the MySQL website.
You must then download the database dump of our project, untar the file and apply it to your database (this process may take some time to complete):
$ tar xvfj ADVISe.tar.bz2 $ mysql -u <your_username> -p <database_to_be_used> < ADVISe.sql
The Processing code is located on the
Processing/ADIVSe folder, and should run on major operating systems. To
download the Processing Sandbox go to the official website.
You need to download the SQLibrary by Florian Jenettand and follow the instructions on the same website.
mysql_settings.txt.template should be copied under the
name it is used by the visualization:
$ cp mysql_settings.txt.template mysql_settings.txt
After that, simply edit it to match your database configuration
Released under the MIT License.