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I would welcome moving the species information down to the <DataNode> level. It could be inherited by the organism set for the full pathway (as is now), but "overwritten" by this information on the node.
I have filed this in the issue tracker: http://developers.pathvisio.org/ticket/1758
I am not sure that is really needed. Not for this pathway in any case. This pathway is multi-species by nature but does not contain specific identifiers from any pathway. Also it actually is a meta-pathway that would link to species specific pathways were we to extend that. While I can think of processes where different organisms are involved these would most often consist of such species specific subpathways. What you proposed sounds like a lot of work for me for a problem that nobody might really have. Or do you have some examples in mind. If we are going into detailing identifiers I would in any case much rather solve that through a state kind of solution that would not only allow to change the species but also things like location, phosphorylation, activation level in general, histone acetylation, CpG island methylation and such.
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