EW7: converting metabolite Labels into DataNodes in WikiPathways GPML

Hypothesis: The GPML format has sufficient information to convert a metabolite encoded as a Label into a DataNode with identifier

Start date: 2014-09-04 End date: 2014-09-06

Description:

The GPML format is used by WikiPathways to internally store pathways. The format is human-readable, allowing for adding missing information. Particularly, it can be used to convert a list of metabolites as <Label> elements as <DataNode> elements. Lists of potential <Label> elements to be converted is outlined in other experiments, such as EW6.

For example:

<Label TextLabel="Acetyl-CoA" GraphId="c7c">
  <Graphics CenterX="150.0" CenterY="640.0" Width="90.33333333333333" Height="19.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="12" Valign="Middle" />
</Label>

This can be converted into:

<DataNode TextLabel="Acetyl-CoA" GraphId="c7c" Type="Metabolite">
  <Graphics CenterX="150.0" CenterY="640.0" Width="90.33333333333333" Height="19.0" ZOrder="28672" FillColor="ffffff" FontWeight="Bold" FontSize="12" Valign="Middle" />
  <Xref Database="ChEBI" ID="CHEBI:15351" />
</DataNode>

Methods

  • Open a WikiPathways page in the MediaWiki edit mode
  • Remove one or more <Label> elements to convert
  • Convert the start and end tag from Label to DataNode
  • Add the Type=”Metabolite” attribute (with value)
  • Add a <Xref> child element, preferable with identifier for that metabolite
  • Place the new <DataNode> elements just above the first <Interaction> element

Report 

Many pathways have been update using this approach in the past, but I had not previously written up the method I used. In the past few days, these are example pathways updated this way:

When there are many <Labels> to be converted, I commonly use a plain text editor and “replace” functionality.

It should be noted that graph identifiers do not get changed, so that links between elements in the GPML are preserved.

Conclusion: This method requires experience with manually editing XML files; the risk is that you break the GPML file, though the WikiPathways interface does validate the file before saving against the GPML XML Schema.

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