CellDesigner export: could duplicate protein references in some cases
The exported CellDesigner "NLRP3_inflammosome_activation" submap from the COVID map (https://covid19map.elixir-luxembourg.org/minerva/?submap=947) has two <celldesigner:protein>
elements with name "ASC" (p_s_id_sa103 and p_s_id_sa104). This seems to be problematic for CellDesigner (when trying to edit the second <celldesigner:protein>
from the list of Proteins, we get an error saying "Same named protein exits. please rename"). Also, <species>
s_id_sa103 has <celldesigner:proteinReference>
p_s_id_sa103 and a <celldesigner:modification>
with id "rs1", while p_s_id_sa103 has a unique <celldesigner:modificationResidue>
with residue "rs2", which is not compatible. p_s_id_sa104 has however also a unique <celldesigner:modificationResidue>
, with id "rs1". The file that could be the source for this map (https://git-r3lab.uni.lu/covid/models/-/blob/master/Curation/Inflammasomes/NLRP3_Activation_stable.xml) does not have this <celldesigner:protein>
duplication.