To store the layout in the SBGN-ML

[IgorRodchenkov]

Dong Xiaoxi emailed:

I find the pathway layout in Pathway Commons web page looks pretty good. For example this one, http://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Fpanther.pathway%2FP00001 But when I downloaded the SBGN-ML file from this web page, there is no coordinated for the nodes (x and y are all 0). Is there any way to get the layout information so users can further modify the SBGN-ML files based on the current layout? I also found that when you open the same link using different web browsers such as Chrome (left) and Firefox(right), the layout is different (I think the Firefox version is better). How did this work? Thank you!

To export the coordinates within SBGN-ML a new micro service is required (could be either part of cPath2 or factoid-converters...)

[nvelden]

Any update on this? When I download the SBGN-ML files the x and y coordinates are still 0.

[IgorRodchenkov]

apps.pathwaycommons.org layout that you see on the web page is dynamic and not based on the sbgn or stored coordinates data, a.f.a.i.k.

When you select SBGN-ML from the download options, the web app calls PC2 web service, e.g. https://www.pathwaycommons.org/pc2/get?format=SBGN&uri=http%3A%2F%2Fidentifiers.org%2Fpanther.pathway%2FP00001 to grab the BioPAX pathway data and auto-convert to SBGN-ML, but that does not apply any alignment (it used to apply some default layout in the past, before 2018, but that wasn't good and also caused performance/memory issues; thus it was disabled).

You could probably use some SBGN apps/tools (I do not know which) to generate own layout after getting the data. Or you can download the BioPAX data and then convert to SBGN and some default layout (no other options unfortunately) with Paxtools console java app, https://biopax.github.io/Paxtools/

Likely, Pathway Commons web service will not enable the layout for SBGN any soon...