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browser-curator's Introduction

Pathway Browser Portal

The Pathway Browser Portal (PWP) is Reactome’s primary means of viewing and interacting with specific pathways. Reactome is a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways aiming to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.

Overview of the Pathway Browser Portal

PWP version 3 features the following improvements:

Re-designed user interface with
  • Cleaner and more user-friendly layout.
  • Colour-consistent look and feel.
Improved user experience
  • Visual feedback for every user action.
  • Control of the flow of information by the zoom level.
  • Improved search functionality.
  • Animation to help the user maintain context.
  • Faster loading.

This video provides a short introduction to the main features of the tool, which is available in Reactome at http://www.reactome.org/PathwayBrowser/

Reactome Pathway Browser 3.2 - Short introduction

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browser-curator's Issues

Pathway rendering issues with nested components

In this pathway, there are rendering issues when there are components inside a component. It looks like this in the pathway browser:

screen shot 2015-04-17 at 10 33 38 am

However, behind Acrosin Heavy:light chain for example, there are two not visible but rendered components. You can tell by looking at the xml:

<org.gk.render.RenderableProtein id="270" reactomeId="1297304" schemaClass="EntityWithAccessionedSequence" position="494 384" bounds="450 367 88 34" textPosition="451 373">
  <Properties>
    <displayName>ACR(43-343)</displayName>
  </Properties>
</org.gk.render.RenderableProtein>
<org.gk.render.RenderableProtein id="271" reactomeId="1297342" schemaClass="EntityWithAccessionedSequence" position="581 383" bounds="544 368 74 30" textPosition="552 366">
  <Properties>
    <displayName>ACR(20-42)</displayName>
  </Properties>
</org.gk.render.RenderableProtein>
<org.gk.render.RenderableComplex id="269" reactomeId="1297314" schemaClass="Complex" position="535 391" bounds="449 366 173 51" textPosition="453 396" bgColor="204 255 255">
  <Properties>
    <displayName>Acrosin Heavy:light chain</displayName>
  </Properties>
  <Components>
    <Component id="270" />
    <Component id="271" />
  </Components>
</org.gk.render.RenderableComplex>

And in a similar issue in the same screenshot, Zona pellucida complex should have 5 components in it but we only see 2 and they are oddly overlapping - making the whole thing illegible.

<org.gk.render.RenderableComplex id="45" reactomeId="1297292" schemaClass="Complex" position="686 398" bounds="654 323 65 151" textPosition="654 439" bgColor="204 255 255">
  <Properties>
    <displayName>Zona pellucida</displayName>
  </Properties>
  <Components>
    <Component id="37" />
    <Component id="40" />
    <Component id="44" />
    <Component id="202" />
    <Component id="414" />
  </Components>
</org.gk.render.RenderableComplex>

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