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Deploying the PRIDE BioMart Alongside a Local PRIDE Installation

Introduction

BioMart is developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL).

For quick help with the BioMart interface, linked both from here and directly from the  PRIDE BioMart page itself, you will find a short help page (linked from the Help button at the top of the page) and a Mini Tutorial describing how to build and run a query on any BioMart. (Install Adobe Flash to view this tutorial)

BioMart allows you to retrieve public PRIDE data from a query-optimised data warehouse that is synchronized with the main PRIDE database each week. The BioMart interface allows you to build simple or complex queries, with total control over both how the data is filtered (to restrict which records are included) and also which attributes (equivalent to columns in a spreadsheet) are included in the results. This allows you to avoid the need to search through a massive table of results, much of which may be irrelevant to you, and focus specifically on the information that is important.

Downloading PRIDE BioMart

Two sets of files need to be downloaded to create a PRIDE BioMart. The PRIDE specific materials can be downloaded from the PRIDE Google Code download page.

Follow the link and download the latest "PRIDE BioMart" file release. (tar.gz file). Save this to a suitable location that will be referred to as [PRIDE_BIOMART_SOURCE] from now on.

You will also need to download the latest BioMart web application. Instructions for doing this are fully documented by the BioMart development team and are linked from the appropriate section below.




Page Contents


Additional PRIDE BioMart Documentation

Creating the BioMart Database Schema

BioMart uses a separate database schema to the main PRIDE database schema. The BioMart schema follows the BioMart guidelines to create a query-optimised 'inverse star' schema. This schema is created and populated by an SQL script that selects public data from the main PRIDE schema.

To allow this script to work, the BioMart schema should be located on the same database server as the main PRIDE schema. Configuration for MySQL is currently available.

For the PRIDE BioMart installation at the EBI, we are currently making use of two BioMart database schemata that are swapped each week (or immediately following a large submission of public data to PRIDE). This helps to ensure that the BioMart service is down for a very short time (perhaps a minute) between updates. It is recommended that a similar mechanism is adopted elsewhere.

A complete SQL script is available to create and populate these schemata. (The scripts begin with DROP TABLE IF EXISTS statements for all of the data tables in the mart schema, so you can refresh the entire schema by running this script alone.) The script is included in the code download in the following folder:

[PRIDE_BIOMART_SOURCE]/sql/production_scripts/complete_update_pride_mart_template

Before use you will need to use a text editor with a global search and replace function to insert the correct names for your main pride schema and the biomart schema as follows:

  • Replace all occurences of MAIN_PRIDE_SCHEMA with the correct schema name.
  • Replace all occurences of PRIDE_BIOMART_SCHEMA_NAME with the correct biomart schema name.

You must run this script under a MySQL login account that has (as a minimum) SELECT privileges on the main PRIDE schema and SELECT, INSERT, DELETE, CREATE, DROP, REFERENCES and INDEX privileges on the BioMart schema.

You should then be able to run this script using the MySQL command line client or a GUI client that allows you to run SQL scripts. This may take a few minutes or even longer depending on the size of your main PRIDE database.

At the end of this process you should check that you have created and populated the BioMart tables as defined in the script in your BioMart schema. Note that some tables may not be populated depending on the data in your main PRIDE schema.

Installing the MartView Web Application and MartEditor Tool

The process of installing MartView and MartEditor is documented in detail at http://www.biomart.org/install.html. MartView is the BioMart web application and web service. MartEditor is also required to allow you to load and configure the user interface from the PRIDE BioMart scripts.

It is recommended that as a minimum you read the entire 'Quick Install Guide' that is available from this page and follow the instructions to install the Perl modules from CPAN and the MartView and MartEditor software from CVS.

Once you have completed the installation of MartView and MartEditor, return to this page to continue the installation of the PRIDE BioMart system.

Configuring the MartView Web Application

Configuring the PRIDE BioMart interface with the MartEditor tool

Following the instructions in the BioMart 'Quick Install Guide', start the MartView application. This is a Java application, so please check that you have a correctly configured Java virtual machine installed. You will need to enter your BioMart database connection details to allow this to work, as illustrated in the example dialogue box below.



Once you have successfully connected to the BioMart using the MartEditor tool, you next need to install the interface definition. This is in the form of two XML files:

[PRIDE_BIOMART_SOURCE]/interface_definition_xml/pride_template.template.xml
[PRIDE_BIOMART_SOURCE]/interface_definition_xml/pride.xml

On the MartEditor tool, select the menu "File"..."Upload All". Accept the warning message by clicking on "Yes".

Now browse to the interface_definition_xml folder, hold the CTRL (PC) or Apple (Mac) key and select both the pride_template.template.xml file and the pride.xml file. Click on "Open". It will take a few seconds for the user interface definition to be loaded into your BioMart Database.

You must now select the menu "File"..."Update All". Wait a few seconds while this update completes.

Now the default user interface definition has been loaded and updated, you must now edit this definition to tailor it to your local installation.

Select the menu "File"..."Import". A window will appear with a 'tree' view of the definition on the left and detailed configuration displayed on the right. There are several points in this definition that are specific to the EBI installation of BioMart that you must modify. These are detailed below.

  • It is quite possible that you will see a second entry on the tree view on the left entitled "FilterPage: new_filters" that is not shaded (light grey). If this appears (as illustrated below) you should right-click on this item and select the "hide toggle" item. This item should now be shaded.



  • For the "experiment_ac" attribute you must change the "linkoutURL" attribute to point to your local PRIDE installation: (Click image for full size)



  • For the "peptide_spectrum_ref" attribute you must change the "linkoutURL" attribute to point to your local PRIDE installation: (Click image for full size)



Save your changes by selecting the menu item "File"..."Export".

Of course if you are familiar with defining BioMart interfaces, you may wish to modify the BioMart interface more extensively. To assist you with this, you may wish to examine the most recent PRIDE BioMart database schema diagram, which can be found in your code download folder:

[PRIDE_BIOMART_SOURCE]/database_schema_design/pride_biomart_schema.png

Database Connection

As described in the BioMart 'Quick Install Guide', it is necessary to create a MartRegistry.xml file that defines the connection to the BioMart database. Your mart registry file should be based upon the following, replacing all the items in square brackets with the correct configuration for your BioMart database:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
        databaseType="mysql"
        host="[MYSQL_SERVER]"
        port="[MYSQL_SERVER_PORT_NUMBER]"
        database="[PRIDE_BIOMART_SCHEMA_NAME]"
        schema="[PRIDE_BIOMART_SCHEMA_NAME]"
        name="pride"
        displayName="PRIDE BioMart"
        user="[DATABASE_USERNAME]"
        password="[DATABASE_PASSWORD]"
        visible="1"
        default="1"
        includeDatasets=""
        martUser=""
        />
</MartRegistry>

You are now ready to run your PRIDE BioMart by following the instructions in the BioMart 'Quick Install Guide'.

Note that your PRIDE BioMart will have the default BioMart look and feel. If you wish to 're-skin' your BioMart to look like the EBI PRIDE BioMart (or a modified version of this) you will need to add / replace the configuration for the MartView with the files listed below and included in the PRIDE BioMart download. (It is recommended that you back up any configuration files that you are replacing). The paths of the files in the download package are the same as the paths of the files in the MartView folder.


Path / File New or replacement
[PRIDE_BIOMART_SOURCE]/martview_files/conf/templates/default/biomart.tt Replacement
[PRIDE_BIOMART_SOURCE]/martview_files/conf/templates/default/header.tt Replacement
[PRIDE_BIOMART_SOURCE]/martview_files/conf/templates/default/footer.tt Replacement
[PRIDE_BIOMART_SOURCE]/martview_files/htdocs/martview/images/logo_biomart_medium.gif New
[PRIDE_BIOMART_SOURCE]/martview_files/htdocs/martview/images/pride_logo.jpg New

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