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This can't be true. I've used interproscan a gazillion time on plant species and never have seen this behaviour.
Can you post some more info on this: which species, exact interproscan command line, ... things like that.
For example, if Pathway analysis is enabled in InterProScan then it provides for Reactome a Human id
R-HSA-5689880which can be viewed here. However, I would prefer that the software uses Plant Reactome. Is there a way to change InterProScan behaviour?Ah, I see, in that sense.
No, I don't think you can change that. The way this is handled by interpro is that some domains (or combinations of) are linked to a certain pathway (or GO label, same system) and if the interpro people only added the human pathway info then that is indeed what you will get back (in some cases this is not a real problem as certain pathways will be present in lots of organisms for instance). From a domain hit you can not always deduct the species you're dealing with so it can't suggest a certain phylum based on that. If a certain domain is only present in certain species then yes it can be more precise.
I'm not sure which domain (protein) we're talking here but you can always go to the interpro website , look up that specific domain and see it's metadata.
Might also be good to perhaps inform the interpro people of this. I would be interested to hear what they say about it.