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

Hello again,

I am very happy to announce that bio models have been integrated into the sbml plugin. This enables the user to search the bio models from the bio models database and import them into the pathvisio editor.

There is a very good web service which is provided by the biomodels website. I used this web service to integrate the bio models into the plugin. In the start, I was hit by many road blocks, but eventually I was successful in completing the feature enhancement.

Now we can search the bio models based upon different terms such as “Bio model Name“, “Person name i.e., the Encoder /Author Name“,”Publication Title/Id“, “CHEBIId” and finally “Uniprot Id“.

Refer: BioModelPanel.java

The following screen shots depicts the functionality of the bio models integration feature:

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Figure 1: Bio models Import Button[Highlighted part ].

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Figure 2: Bio model Panel.

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Figure 3: Tool tips for every search field.

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Figure 4: Search by Bio model Name. Here: “Tyson1991 – Cell Cycle 6 var“.

 

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Figure 5: Search result displayed in the table bottom.

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Figure 6 : Opening the selected bio model. Here : http://www.ebi.ac.uk/biomodels-main/BIOMD0000000005

 

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Figure 7 : Imported SBML Model.

 

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 Figure 8: Searching by Publication Name/Id . Here: ‘sbml‘.

 

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Figure 9 : Search by CHEBI Id. Here: “24996“.

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Figure 10: Search by Person/Encoder/Author name. Here : ‘Rainer‘.

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Figure 11 : Search by Uniprot ID. Here :”P04637 “.

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Figure 12: Searching with empty strings gives you an error.

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Figure 13: Searching with invalid strings will give you a message.

Note: If you search with two search terms i.e., for example Publication Name and Biomodel Name and press search, the two results will be added up and showed in the results table.

Cheers,

Sri Harsha.P

Hi,

Last week my task was to integrate the bio models into the plugin using its web service. But I could not complete it as I was struck with several bugs in my code. The SBML import was not working which in turn affected the visualization of the components of the sbml file feature because visualization of the components depends on the SBML file import. The other problem I had was the duplication of the buttons which are involved in the plugin. It looks like the following:

Untitled

As you can see in the image, SBML side pane got repeated twice and the validate,force directed layout buttons too. This was actually affecting the import of the sbml file.

Later, I fixed this issue by clearing the cache. I removed the existing data which was stored in the AppData/Pathvisio which made the magic. This was a new thing which I learned.

Though my import was working fine, the visualization of the components of the sbml file was not working then.

The problem is that the imported file was not getting set to a doc variable which resulted in the bug. This commit fixes it.

I added comments to the code and added licenses. I haven’t finished the integration of the bio models yet. I will be working on it and will complete it in few days.

Cheers,

Sri Harsha.P