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.