Errors importing SBML, SBGN and xml files

[Jordan Langston]

Hello,

I just downloaded Pathvisio on my mac a couple weeks but am encountering a couple errors I'm unsure how to address. I want to import pathways from non-wikipathways (i.e. REACTOME, PANTHER, KEGG), but when I export the REACTOME pathways for example as either SBGN or SBML files, I receive the errors:

#SBML error:

Exception during conversion

See error log for details

class java.xml.stream.FactoryConfiguration Error

#SBGN error:

class java.lang.reflect.InvocationTargetException:null

See error log for details

class org.pathvisio.core.model.ConverterExpression

Also, can you merge pathways into a larger map in Pathvisio?

Thank you

[Martina Summer-Kutmon]

Dear Jordan,

Sorry for the late reply. Somehow I missed this message. 

For SBGN and SBML, we have plugins in PathVisio that need to be installed before you can open any files (Plugins > Plugin Manager). However, I want to note here that both of these plugins are not able to open all versions of SBGN / SBML and it is on our task list to update them. So I am sure that not all files can be opened.

Regarding Reactome pathways, we converted them to GPML and they can be opened in PathVisio from WikiPathways directly. 

Regarding the merging: In theory, you can copy multiple pathways into one in PathVisio by opening PathVisio multiple times but I am not sure that is the best approach. I would probably merge the pathways in e.g. Cytoscape but it depends a little on what you want to have exactly. 

Hope this helps!

Best regards,

Tina

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com