Submission to BioPAX/SBGN: Missing types

[jvwong]

Looks like no edge created for “protein activates protein” and “chemical activates protein” cases.

Here is a factoid document created from http://unstable.factoid.baderlab.org. After submitting it to PC we have this result in http://appsbeta.pathwaycommons.org.

See that the interaction between FSHB and IGF1 (protein activates protein) and the one between Estradiol and LEP (chemical activates protein) are missing in the resulting graph.

[IgorRodchenkov]

@jvwong @metincansiper @maxkfranz

The BioPAX looks just fine - as we designed and expected it. So, this must be either the paxtools/sbgn-converter (java) issue or sbgnml-to-cytoscape npm module issue.

I could create an issue and try to test and fix if it is in Paxtools.

FYI: http://web.newteditor.org/ and http://www.cs.bilkent.edu.tr/~ivis/SBGNViz.js both do much worse job than app-ui using the same input SBGN model.

[IgorRodchenkov]

I confirm that it's a Paxtools/sbgn-converter issue BioPAX/Paxtools#41
(After fixing Paxtools, the PC10 server(s) must be re-built and restarted in order this issue to be fixed as well).

[IgorRodchenkov]

95% fixed :) try it.
I also noticed that in case of "BMP2 activates JUN via phosphorylation", you cannot see "inactive"/"active" states on the JUN, but can see "!phosphorylated" and "phosphorylated"...

[jvwong]

I also noticed that in case of "BMP2 activates JUN via phosphorylation", you cannot see "inactive"/"active" states on the JUN, but can see "!phosphorylated" and "phosphorylated"...

Possibly related - PathwayCommons/sbgnml-to-cytoscape#22

[IgorRodchenkov]

Now it looks as follows:

in factod -

in the apps: