Editing and saving KEGG pathway files

Question

[justp]

I wanted to know if there is a way to take xml files from KEGG and be able to add proteins in a pre-existing group in the pathway, then save that in a new xml file that retains the existing xml information with the new changes. I've been running into trouble with being able to save the xml files using KEGGscape or CytoKegg apps in Cytoscape. I end up with missing information, such as group id.

I'm trying to work with some xml files in KEGG to make changes that incorporate information (i.e. specific proteins) that isn't included in the pathway, but might be useful for my own needs. I want to analyze and compare the differences later on using the original xml files as a base of comparison.

Answer 1

[theobroma22]

I've never done this, but I have worked with XML files, and needless to say as you may know the KEGG pathways are well-curated based on the literature. However, you can open the xml file in a text editor like gedit or notepad. I'm looking at one now...Then you will see the ids in the child node under the parent pathway node. Maybe you can insert your id there, and save it? Also, you may need to convert the protein ID to the gene ID cause I don't see the protein ID in my file, but if your xml files have protein ids I don't see why it won't work. All I know is that you can add to the xml file, but make sure all other required info is added as well so it is read without errors. Sorry this doesn't help much.

[justp]

Thanks! Just wanted to update this. There is information that is likely hard coded in the PNG file or whatever that isn't coded in the xml file, so there is some information that is visible on the image found in the PNG file on the KEGG website, but isn't in the xml file. I've tried what you said and I'm able to add a node or some other kind of annotation, but it's a bit of a tedious process. Cytoscape doesn't seem to work well with saving and updating KEGG files, but I could be doing something wrong.