Hello Everyone,
This is the first blog entry on my GSOC project "Pathway Comparison Plugin" and also my very first blogging experience. I will write up an entry every week reporting about the project status.
The current status:
1. During the project proposal I worked on a window (JFrame) which would display 2 Pathways outside PathVisio's main window. This initial prototype just loaded two pathways from 2 hard-coded locations inside the JFrame's internal frames, but there has been an issue loading and displaying 2 different pathways in the window simultaneously. The Pathway objects (corresponding to the 2 pathways) would load fine, but the VPathway objects required to draw the pathways inside the 2 internal frames have an issue. I am working on it. At the moment, it seems that PathVisio allows only one VPathway object (recently loaded one) to be used for drawing.
2. I have created a PathVisio plugin which allows the user to choose 2 pathways through two "Load Pathway" buttons and a "Compare" button to compare the Pathways. Hitting the compare button brings up the "Pathway-Comaprison" window mentioned above. This window has 2 internal frames to display the 2 loaded pathways adjacent to each other, but due to the VPathway object issue, it displays only the last loaded Pathway in either one of the internal frames. I also plan to include one more partition (another internal frame) which would display the comparison results (the matching pathway elements in the 2 pathways)
3. The compare button does the comparison of the two Pathways (compares the 2 'Pathway' objects) after loading and display the two pathways. The comparison includes comparing the DataNodes (<DataNode> tag) and interactions (<Line> tag) in the two pathways.
I have almost finished basic DataNode comparison which compares Datanodes in one Pathway to Datanodes in the other based on the DataNode types (Metabolite, Gene, Protein etc). Thus, Metabolites in one pathway are only compared against Metabolites in the other. This is the first line of comparison. This way we weed out unnecessary comparisons amongst Datanodes which differ in their types.
The second line of comparison involves comparing <Xref> tag under <DataNode> using BridgeDB as the Id mapper. For testing purposes, I am currently comparing GraphId attribute of the DataNodes in the 2 pathways. DataNodes of the same type and matching GraphIds are highlighted in blue. I will change this to do BridgeDB Xref based comparison soon. I have already tested out how Id mapping works in BridgeDB by checking the mapping of 2 Xref Ids corresponding to a particular gene using a BidgeDb tutorial.
4. I will be discussing "comparing the interactions in the two pathways" with my mentor tonight as there is clarification needed on the subject before I could start writing code.
Below is a screenshot of "Pathway Comparison Plugin" comparing 2 pathways:
As seen , pathway #1 is not loaded in the internal frame due to the VPathway Object issue mentioned earlier above.
The only difference between the 2 pathways is the DataNode of type "GeneProduct" (the unhighlighted DataNode in the screenshot) which has different graphIds in the 2 pathways. All others have matching graphId and types in both the pathways.
The DataNodes highlighted using blue are similar in both Pathways. The one not highlighted has different graphIds in the 2 pathways.
This is the first blog entry on my GSOC project "Pathway Comparison Plugin" and also my very first blogging experience. I will write up an entry every week reporting about the project status.
The current status:
1. During the project proposal I worked on a window (JFrame) which would display 2 Pathways outside PathVisio's main window. This initial prototype just loaded two pathways from 2 hard-coded locations inside the JFrame's internal frames, but there has been an issue loading and displaying 2 different pathways in the window simultaneously. The Pathway objects (corresponding to the 2 pathways) would load fine, but the VPathway objects required to draw the pathways inside the 2 internal frames have an issue. I am working on it. At the moment, it seems that PathVisio allows only one VPathway object (recently loaded one) to be used for drawing.
2. I have created a PathVisio plugin which allows the user to choose 2 pathways through two "Load Pathway" buttons and a "Compare" button to compare the Pathways. Hitting the compare button brings up the "Pathway-Comaprison" window mentioned above. This window has 2 internal frames to display the 2 loaded pathways adjacent to each other, but due to the VPathway object issue, it displays only the last loaded Pathway in either one of the internal frames. I also plan to include one more partition (another internal frame) which would display the comparison results (the matching pathway elements in the 2 pathways)
3. The compare button does the comparison of the two Pathways (compares the 2 'Pathway' objects) after loading and display the two pathways. The comparison includes comparing the DataNodes (<DataNode> tag) and interactions (<Line> tag) in the two pathways.
I have almost finished basic DataNode comparison which compares Datanodes in one Pathway to Datanodes in the other based on the DataNode types (Metabolite, Gene, Protein etc). Thus, Metabolites in one pathway are only compared against Metabolites in the other. This is the first line of comparison. This way we weed out unnecessary comparisons amongst Datanodes which differ in their types.
The second line of comparison involves comparing <Xref> tag under <DataNode> using BridgeDB as the Id mapper. For testing purposes, I am currently comparing GraphId attribute of the DataNodes in the 2 pathways. DataNodes of the same type and matching GraphIds are highlighted in blue. I will change this to do BridgeDB Xref based comparison soon. I have already tested out how Id mapping works in BridgeDB by checking the mapping of 2 Xref Ids corresponding to a particular gene using a BidgeDb tutorial.
4. I will be discussing "comparing the interactions in the two pathways" with my mentor tonight as there is clarification needed on the subject before I could start writing code.
Below is a screenshot of "Pathway Comparison Plugin" comparing 2 pathways:
As seen , pathway #1 is not loaded in the internal frame due to the VPathway Object issue mentioned earlier above.
The only difference between the 2 pathways is the DataNode of type "GeneProduct" (the unhighlighted DataNode in the screenshot) which has different graphIds in the 2 pathways. All others have matching graphId and types in both the pathways.
The DataNodes highlighted using blue are similar in both Pathways. The one not highlighted has different graphIds in the 2 pathways.
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