phpDAVIDws

A class-based PHP platform for DAVID web services

Functional annotation is one of the fundamental step in downstream analysis in genomics and proteomics to give biological meaning to genes and proteins.

DAVID (database for annotation, visualization and integrated discovery), is a web-based bioinformatics platform (http://david.abcc.ncifcrf.gov), that provides tools for functional interpretation of large lists of genes/proteins (Huang et al., 2009).

DAVID used to have a URL based access to their knowledge base. It gives limited control for the user to communicate with the DAVID website to get biological meaning for the list of genes/proteins. Due to its limitations, DAVID team recently developed a web service interface (DAVID-WS) by giving a full control over all its functionalities (Jiao et al., 2012). To connect and communicate with the DAVID web service bioinformaticians, biocurators need a client which is developed in a programming language of their interest. For some programming languages, DAVID-WS clients have been already made available including; Python, Perl, Matlab, Java (Jiao et al., 2012) and R (Fresno et al. 2013). PHP is one of most used web development programming language to develop online bioinformatics tools and a databases. But, currently there is no PHP based client is available to access the DAVID web services. Hence we developed a class-based PHP interface to access all the DAVID-WS functionalities in a PHP environment.

Installation

To install, simply download phpDAVIDws and include the autoload.php to where you want to use the service.

require 'phpDAVIDws/david_autoloader.php';

How to use

Users are required to register before using this service If you are a new user, please register at http://david.abcc.ncifcrf.gov/webservice/register.htm.

require 'phpDAVIDws/david_autoloader.php';

$service = new DAVIDWebService();
$email = "yourname@yourorganization.org";

$request = new authenticate($email);

//it will return a authenticateResponse object
$response = $service->authenticate($request);

if($response->getReturn() == "true"){
    //perform anaotation
}
else{
    //Register or check your email.
}

phpDAVIDws Documentation

A detailed documentation can be found here: http://bioinfo.au.tsinghua.edu.cn/software/phpDAVIDws/doc/