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Have we though about mechanisms for multispecies pathways? Can we maybe set the species to "none" or "unknown" to at least signal something special is going on. (or will that make them unfindable?)
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
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