Node names and annotations

[CatherM]

Hello Aurelien Dugourd, Attila Gabor,

I am using COSMOS to generate networks based on transcriptomic and metabolomic data. I then analyze the networks in Cytoscape.
I have a few question regarding names and annotations of nodes.

Firstly, there are a few situations in which nodes are connected to another node that represent the same molecule (or so I presume). For example FH here is connected to Enzyme7542__FH and Enzyme8947__FH. Is there a reason for these numbers all representing the same enzyme?

Secondly, when the parameter ‘depth’ is made larger, I find odd names, ones that start with ‘orphanReac’ and/or end in ‘_reverse’ (e.g. Enzyme177300002__orphanReacPHEt2m
or Enzyme7347__GOT1_reverse, or Enzyme941__orphanReacILEtmi_reverse).

Is this because the network did not finish running due to time restraint, or are these node names correct and do I need more information to help interpret them?

Thank you in advance for the amazing tool, vignettes and help.

Kind regards,
Cathy.