A Web Service for Generating Protein Interaction Networks from

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A Web Service for Generating Protein Interaction
Networks from Proteomic Databases Masters
Project Presentation 12/15/05
Vamshi Chilukamarri Dr. M.
Zubair / Dr.Alex Pothen
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• Introduction
• Background..Research..Collection of Data
• HPRD database. Analysis of data and realizing the
• idea
• Preprocessing of HPRD data
• Construction of HPRD Network
• Exposing the Network as Sub graph query XML Web
  service
• Develop a client to query the service

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Introduction

• Protein Databases
• Examples - Protein Databases
• The problem (image)
• Solution, a prototype Approach using HPRD
• Background
• Pre processing
• Creation of Network Graph
• Sub Graph Module as Webservice
• A use case (a list of proteins as input) to test.

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Problem with Large Protein Network
Yeast DIP Reliable Network
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Background..Research..Collection of data

• HPRD Protein Database
• http//www.hprd.org
• This database represents a centralized platform
  to visually depict and integrate information
  pertaining to domain architecture,
  post-translational modifications, interaction
  networks and disease association for each protein
  in the human proteome.

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HPRD Database

• HPRD database (http//www.hprd.org)
• Download the HPRD
• Understand the XML

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Pre processing of HPRD data

• Create Network Graph of entire HPRD.
• As the xml data consisted of interactions among
  various proteins, we used Pajek format to store
  the network graph in the form of a file.
• I divided the task into two tasks.
• Collection of protein properties. The properties
  specifically were protein names, molecular
  properties, gene symbols, localized properties.
• Creation of actual HPRD network.

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Construction of HPRD Network

• The property files created during the process
  are
• expression_sites.properties
• gene_symbol.properties
• Molecular_Function.properties
• proteinNames.properties
• cellularProps.xml a file which contains
  localized GOID, localized titles
• The network file created is
• completehprd.net

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Sub Graph Module

• Program to accept proteins as inputs and query
  the large network
• Construct the Sub Graph
• The creation of sub graph is possible with the
  help of JUNG (Java API for Universal Network
  Graphs).
• Apply the 1st Neighborhood Filter over the
  resultant sub graph
• Expose the Sub Graph module as a XML Web Service.
• This webservice layer is developed and deployed
  over the Axis container inside Tomcat 5.0 Web
  container.
• The JUNG is an open source API
  (http//jung.sourceforge.net/). This API also has
  various utilities for Visualizing network graphs,
  filtering the graphs Using K Neighborhood utility
  classes.

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Develop a client to query the service

• Create a Client to call the Webservice.
• Client should accept input as a list of proteins.
  In this case hprd ids.
• Send the input (list of proteins) over the wire
  to the Webservice.
• Webservice processes Sub graph generation
  procedure for the given inputs.
• Returns the 1st neighborhood sub graph.
• Client displays the subgraph in a GUI interface
  and also saves the subgraph and properties in a
  directory for later use.
• Use case with sampleinput.txt file which is a
  list of protein IDs

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Future Goal
HPRD
F E D E R A T I O N
XML Webservice
Query for Protein Information in any database
Client
DIP
STRING
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• Thanks to..
• Dr. Alex Pothen
• Dr. Zubair
• Dr. Chris Osgood
• Emad Ramadan