PD2AF conversion problem in Reactome maps

[hasanbalci]

The SBGN PD files loaded from the Reactome database cannot be properly converted to AF using the PD2AF converter. It appears that these files contain label tags under process glyphs, which prevents proper conversion. If label texts are replaced with an empty value or the labels are removed entirely, the conversion works properly.

According to the SBGN PD specification, process glyphs shouldn't have labels, and SBGN visualization tools are also designed not to show labels on process nodes. However, I think Reactome uses them for annotation purposes.

Here is a sample case:

• input map

• a proper conversion (in case that process nodes don't have labels in SBGN file)

• incorrect conversion (in case that process nodes have labels in SBGN file)