Project Updates


The Proteome Browser - A Software Resource for the Chromosome-Centric Human Proteome Project

posted May 2, 2013, 9:09 PM by TPB Administrator   [ updated May 5, 2013, 6:08 PM ]

The Proteome Browser is a web-based portal to the human proteome developed to support the efforts of the Australian/New Zealand consortium in the Chromosome-centric Human Proteome Project (C-HPP). This portal, built in conjunction with the Proteomics community, includes a data integration and analysis software system that integrates up-to-date pertinent information from multiple large international biological databases that house genomic and protein data, and assembles this information into a format suitable for a global proteomics effort of the kind proposed by the C-HPP.

The Proteome Browser integrates protein data from a number of source systems including Ensemble, GPM, The Human Protein Atlas and NeXtProt. The data collections from this portal are also made discoverable through ANDS' Research Data Australia.

The Proteome Browser provides a web interface that is designed to display an overview of the current evidence supporting the identification of various gene products across the chromosome, such as protein expression, modification and disease association, with the ability to drill down to the original data. The design of the portal allows for easy addition of both new data sources and data categories.




The ‘traffic light’ representation of proteomic data, includes an X axis that relates to each gene (i.e. protein) ordered by default in the order found on the Chromosome, and the Y axis relates to the types of evidence that support the identification of proteins. The traffic light system is used to indicate cases where different types of data exists or do not exist for a particular protein.




Various aspects of the underlying contributing information are available for further analyses using clustering and drill down/through capabilities. The user interface is dynamic, showing relevant information by providing the ability to filter; and also provides links to external systems where appropriate.

The Proteome Browser has produced significant benefits for Australian and international proteomic researchers by:
  • Providing an extendable platform to support mining of new and existing proteomics data for novel research outcomes
  • Supporting the C-HPP initiative by providing a visualisation tool for the ‘Trans Proteomic Pipeline’, the standard analysis pipeline for proteomic data
  • Enabling researchers to identify all predicted proteins and their isoforms, followed by cataloguing and analysis of the associated data
  • Enabling the integration of data from different sources to provide a cohesive view of the existing proteomic landscape which includes
    • Creating a portal to the human proteome
    • Delineating the complex proteome in the context of the linear genome
    • Enabling comprehensive analysis by supporting the interrogation of multiple genes simultaneously
    • Providing a measure of data confidence
  • Facilitating the linking of data into a common research data space, through the Australian Research Data Commons.

User feedback driving improvements in the Proteome Browser

posted Mar 17, 2013, 10:23 PM by TPB Administrator   [ updated Mar 27, 2013, 7:16 PM ]

Introduction

The Proteome Browser (TPB) is an initiative of the Australia/New Zealand Chromosome 7 consortium of the Chromosome-centric Human Proteome Project (C-HPP).

TPB is currently being developed by the Monash University e-Research Centre with funding for the initial phase of development provided by the Australian National Data Service.

The ‘ease of use’ of the browser is an important requirement for the success of the project. In order to assist in this endeavour a usability analysis exercise was conducted. While this blog post provides a summary of the outcome of this exercise, the final report that documents the findings of this study is available here.

Usability testing

Usability testing typically involves a group of participants that represent the end-users of a system systematically working through a set of tasks, while a facilitator observes and conducts an inquiry into participant behaviour.

For the TPB project, 5 researchers from the Genomics and Proteomics fields worked through a set of tasks that closely represented some of the core user tasks. The tasks were developed in collaboration with Dr. Rob Goode (Research adviser of the TPB project).

Participant details

#

Research areas

Familiarity with the system

Test Status

P1

Proteomics

Stakeholder of the TPB project. Was familiar with the purpose and functionality of the system.

Completed

P2

Proteomics

Had trialled the system briefly.

Completed

P3

Proteomics

Had trialled the system briefly

Completed

P4

Proteomics

Had trialled the system briefly. Had seen the system demos during conferences. 

Completed

P5

Genomics

Had no experience

Completed


Executive summary

The survey participants found the Proteome Browser web portal to be a useful visualisation tool for Proteomic data, particularly the Traffic Light Report in both the Summary and Detail modes. While the 'Summary View' provides a high level overview of the proteome along with a colour-coded representation of the underlying data quality, the 'Detailed View' supports drilling down into the underlying data and also drilling through to the original data at the data sources. This approach facilitated the identification of regions of interest in the proteome very quickly to allow detailed analysis of data relevant to these regions

The availability of data for all chromosomes and the ability to filter the traffic light report by chromosomes was seen as a useful feature. The participants also felt that the gene symbol and accession search functionality would be valuable in their research.

The participants felt that the Proteome Browser had successfully demonstrated the application of a traffic light matrix approach to the representation of proteomic data to support the international C-HPP initiative. They identified enhancements to the documentation and user interface that would improve the user experience and new functionality that would support ongoing research.

Usability findings

 What worked

  • ·      Chromosome drop-box(s) in the home page
  • ·      FAQ descriptions
  • ·      The traffic light report (visualization)
  • ·      Gene symbol and accession search functionality
  • ·      Accessing ‘Summary report’
  • ·      Accessing the ‘Detailed view’

Issues

  • ·      Home page too ‘Texty’
  • ·      The term ‘Traffic light’ is not meaningful for new users
  • ·      Participants didn’t notice the ‘More options’ link
  • ·      Participants didn’t understand the data type acronyms
  • ·      Participants couldn’t find the pop-ups that contained the data type and colour code explanations
  • ·      Participants didn’t realize different data types could have different explanations for the colour codes
  • ·      Participants had trouble using the ‘Evidence level data type’ filtering functionality
  • ·      Participants had trouble understanding the traffic light report produced by the ‘Evidence level data type’ filtering functionality
  • ·      Participants didn’t know what to put in ‘Chromosome region’ text boxes
  • ·      Some participants didn’t think the user guide is under ‘Documentation’ navigation item
  • ·      Export accession file format is not clear
  • ·      All participants commented that they do not have much knowledge about the data sources listed (i.e. neXtProt, GPM and HPA)
  • ·      The text ‘summary’ in the detailed view was not meaningful for participants

Requirements

  • ·      Ability to export a list of genes
  • ·      Remove the chromosome dependency
  • ·      Inclusion of where, how and when proteins are expressed
  • ·      Disease based information for proteins
  • ·      Ability to filter the evidence further via:
    • o   Tissue distribution
    • o   Predicted tissue distribution
    • o   Biology
    • o   Diseases
    • o   Promoters
  • ·      Ability to import a list of gene/protein symbols/accessions to the search field
  • ·      Ability to search via Protein name or accession
  • ·      Include UniProt data source
  • ·      Inclusion of transcriptome data.
  • ·      Ability to search Non-coding RNAs and information that are not annotated in the genome
  • ·      Improve confidence in the data presented
  • ·      Ability to see co-expression
  • ·       Ability to conduct an OR type filter using the data type evidence level filters
  • ·      Inclusion of other species in the TPB
  • ·      The ability to search for gene information in gene based databases and linking to the TPB to find out Protein expression evidence
  • ·      Would like to see information similar to the “Saccharomyces Genome database

#andsUserAcceptance #andsOutputs #andsProduct #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

The Proteome Browser mentioned in WIRED

posted Nov 15, 2012, 2:14 PM by TPB Administrator

The Proteome Browser has been mentioned in an article about the Human Proteome in "The WIRED World in 2103" - a 'what's hot in 2013' special issue from WIRED magazine:

   

The full issue is:
• downloadable from within the Wired UK app on iTunes/Kindle/Android
• downloadable from tinyurl.com/wiredworld2013
• on sale in shops now

An article on HUPO 2012

posted Sep 18, 2012, 5:22 PM by Anitha Kannan   [ updated Oct 3, 2012, 4:48 PM ]

The following article in Genomeweb summarises the discussions and outcomes from the HUPO 11th Annual World Congress held in Boston from September 9-13, 2012.

At HUPO 2012, Researchers Look to Prove, Promote Proteomics as Broad Life Sciences Research Tool

September 14, 2012

TPB featured in Australian Life Scientist

posted Sep 13, 2012, 4:33 PM by Anitha Kannan   [ updated Mar 17, 2013, 10:58 PM by TPB Administrator ]

The Proteome Browser was featured in a recent article in Australian Life Scientist in which Prof Ian Smith was interviewed about the C-HPP initiative and The Proteome Browser.

A PDF version of this article is also attached to this post.


#andsContractedDOVs #andsValue #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

HUPO 11th Annual World Congress, Boston 2012, September 9-13

posted Sep 11, 2012, 8:25 PM by Anitha Kannan   [ updated Mar 17, 2013, 10:57 PM by TPB Administrator ]




  

Ed Nice and Rob Goode presenting The Proteome Browser at the HUPO 11th Annual World Congress.

#andsContractedDOVs #andsValue #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

AOHUPO 6th Congress held at Beijing, China (May 5th -7th, 2012)

posted Sep 2, 2012, 8:05 PM by Anitha Kannan   [ updated Mar 17, 2013, 10:54 PM by TPB Administrator ]


Rob Goode, Ed Nice and Mark Baker at the AOHUPO conference in Beijing

#andsContractedDOVs #andsValue #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

The Product

posted Jul 15, 2012, 5:48 PM by Anitha Kannan

The key output from this project will be the development of The Proteome Browser, a visualisation tool that will be a portal to the human proteome, with a genome-based approach for the organisation of the proteomics data.

The Proteome Browser is envisaged to be a portal to the human proteome for the global Genomic, Proteomic and Metabolomic research communities that will delineate the complex proteome in the context of the linear genome. It will provide an intuitive interface to interrogate and integrate, existing and emerging proteomics data. As a visualisation tool, it will enable comprehensive in-depth analysis and show proteins that are mapped in the context of the particular chromosome.

At the completion of this project; all documentation, reports, and presentations will be kept in Monash’s enterprise wiki, Confluence; and all software, including the installation guide and user guide will be kept in Google Code. Software materials will be licensed using GNU GPL v3. Non-software materials will be licensed using Creative Commons; however; the AusGOAL framework may be used, if it is deemed suitable for research use.

To promote the sustainability of the solution, it will be developed using the following principles:
  • Solution development will be led by the related research community
  • The research community (i.e. Proteomics Australia) will own the solution, and not the institution (Monash)
  • The solution will be developed in many simple components rather than a single large amorphous package
  • The solution will be designed and developed in a way that it is relatively easy to install at other research institutions
  • Researchers involved in the project will be encouraged to communicate the benefits of the solution to their community
  • Monash will endeavour to collaborate with other institutions on the development and deployment of components

#andsOutputs #andsProduct #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

How will we know if the project has been successful?

posted Jul 15, 2012, 5:33 PM by Anitha Kannan   [ updated Jul 15, 2012, 5:36 PM ]

Despite multiple large international biological databases housing genomic and protein data, there is currently no single system that integrates up-to-date pertinent information from each of these data repositories and assembles the information into a format suitable for a global proteomics effort of the type proposed by the Chromosome-centric Human Proteome Project (C-HPP).

This project aims to produce a data integration and analysis software system for the C-HPP effort and to make data collections from this resource discoverable through ANDS's Research Data Australia. The Proteome Browser will assist Australian and international efforts in completing a map of the Human Proteome. The mapping of the human proteome, even a partial mapping, will help elucidate biological and molecular function and provide advance diagnosis and treatment of diseases. It’s approach may also be applied to other animals and plants.

This software needs to be:

  • Easy to use
  • A visualisation tool designed to display an overview of the current evidence supporting the identification of various gene products across the chromosome, such as protein expression, modification and disease association, with the ability to drill down to the original data
  • Extensible, to allow for easy addition of both new data sources and data categories

To achieve these objectives we will:

  • Design the software to be ultimately species and chromosome independent, whilst maintaining the initial focus on the development of a resource for Human Chromosome 7
  • Have two Product Owners involved in this project, one representing Proteomic researchers and the other ANDS. The Product Owners will contribute towards the features to be developed and set priorities on when these features are developed. They will also seek guidance from the project’s steering committee.
  • Have a steering group /advisory committee for the project which will comprise of key members from the Australian and international Proteomics community.
  • Ensure that the application is built to a high quality and meets the needs of the researchers via a test strategy that includes unit testing, system testing and integration testing by the development team; followed by user acceptance test by members of the Proteomics research community.
    When the Product Owners select a version for release to the Production Environment, a selection of stakeholders across the Australian C-HPP effort will test the version in the Staging Environment as a part of the user acceptance test of the release to determine if the user requirements have been met.

#
andsQuality #andsValue #andsAssessment #andsCustomers #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

Key Technologies and Features

posted Jul 10, 2012, 8:49 PM by TPB Wiki Admin   [ updated Jul 10, 2012, 8:55 PM ]

The Proteome Browser integrates data from multiple data sources and makes the collections from these sources available to ANDS' Research Data Australia. A high level overview of the software architecture is available @ The Proteome Browser


#andsFeatures #andsFunctions #andsTechnology #andsArchitecture #andsTools #andsApps #fundedByAustralianNationalDataService #DIISRTE #TPB #andsAP32

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