We don't know yet. It's a pretty significant development.
It could all be part of the same causal time loop. Thawne brings Gideon from 2200 (or whenever Thawne is from) to the "present". Barry discovers Gideon and then reverse engineers Gideon for general application (or maybe just for use by the Justice League/Society) with the help of Cisco and Caitlin. So, if Thawne had never brought Gideon back with him, then Barry never would have discovered Gideon and reverse engineered Gideon.
It does seem to be a pretty big leap of logic for Barry to have developed Gideon in the original timeline with absolutely no inspiration or direction. No-one on the show has ever mentioned artificial intelligence and although Barry has an interest in science, I don't think he's ever shown a particular interest in AI before.
Then again, Gideon could be based on some villain or alien technology that Barry encounters in the future, something built by ATOM which Barry then further develops, something built by Mercury Labs, the military or another third party which Barry considers to be too dangerous for general use and "steals" and then further develops. I don't think we have enough information to draw any further conclusions about Gideon's statement that Barry was her "creator" at this time.
