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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 ]


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



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




Had trialled the system briefly.




Had trialled the system briefly




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




Had no experience


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’


  • ·      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


  • ·      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

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