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iVis-at-Bilkent / newt

A web application to visualize and edit pathway models
http://newteditor.org
GNU Lesser General Public License v3.0
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Missing edges after GPML export #732

Closed hasanbalci closed 3 months ago

hasanbalci commented 3 months ago

When we try to export SBGN maps as GPML, we lost some edges during MINERVA conversion. Here is an example:

When we import WP554 pathway WP554.gpml.txt to Newt in SBGN format (by using MINERVA GPML -> SBGN conversion) it works correctly :

Screenshot 2024-07-10 at 17 03 50

If we then export this map as GPML (by using MINERVA SBGN -> GPML conversion) it shows the following in the exported GPML file, in other words it cannot convert those edges:

Screenshot 2024-07-10 at 17 08 28

If we try to import the exported file again (see some of the edges are missing):

Screenshot 2024-07-10 at 17 13 26
hasanbalci commented 3 months ago

It seems that this issue is more related to MINERVA conversion service. MINERVA's GPML->SBGNML conversion allows generating PD+AF maps (as seen in the first image), but its SBGNML->GPML conversion only takes into account PD rules.