Bonjour,

Previously, the annotations of the elements of the sbml model were not shown in the backpage. The Data nodes and the interactions can be annotated as of now and these should be visualized in the back page of the pathvisio editor.

So, this can be achieved by extracting the data source and the id from the annotation tag of the bio model’s xml file and the data source and the gene id should be set. This can be done using the Xref’s.

The annotations for the elements are under the <rdf> tag which is a child of the <annotation> tag. And it is present in the form of an URI.

The URI was something like this rdf:resource=”http://identifiers.org/reactome/REACT_6308”  The annotation id for this element is REACT_6308 and the data source is the reactome from the above URI.

The values after the identifiers.org/ was changing for every URI. Hence I extracted the URI using the annotation.getCVTerms().getResources  and then used the split function to grab the required values.

Then, I have set these two values on the pathway element.

Refer:   annotation commit and PeerModel.java

The following images depicts the functionality of this feature:

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Figure 1: Bio model imported. And no element is selected. See Backpage tab.

 

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Figure 2: The annotation for the selected element is shown in the back page tab.

 

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Figure 3 : The annotation of the selected element is shown in the back page tab.

 

Note: Bio model imported is http://www.ebi.ac.uk/biomodels-main/BIOMD0000000209

 

Vive,

Sri Harsha.P

3 thoughts on “Annotations of the elements are displayed in back page

  1. Very good job!

    Is it also possible to parse out the datanode type ?

    Here the datanodetype of he datanode is unknown (as you see in the backpage header).

    Reply

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