Yes that doc you were reading is out of date. I have actually been updating reactome.db for a while now (with occasional input from Willem). There has been an updated version every release and they are numbered to match the version of reactome that they contain. But after the most recent update (merely a few weeks ago) the reactome folks pulled the denormalized db dumps from their site. And now I can see why since it looks like the most recent denormalized dumps were not actually ever updated to reactome version 50. That's a bummer since it basically means that the most recent package has some stale information in it (which I am working on getting updated). This is the ultimate cause of both of the different problems that Guangchuang has mentioned. These fields are all ones that originate in the denormalized database.
Anyhow, I am currently discussing a solution to this problem with them but the conversation has been proceeding at a pace of about one reply per day and so it still hasn't wrapped up (yet). It all looks hopeful though (the reactome guys are helping me to know more about what their long term future plans are for this data resource). And we are currently discussing the best alternative routes for me to get the information that previously came from their denormalized database. When the conversation has concluded I will make a new updated reactome.db package I will push it online and post about it here.
Unfortunately, I am still waiting for some key replacement data from reactome. On a positive note though, a few days ago the reactome guys emailed me again confirming that they planned to really do this very soon.
It was a long journey, and we will still need a long term solution, since this time they had to generate the file at Reactome, instead of me being able to do it myself. We will continue working together for a better long term solution.
Reactome.db sqlite database was generated with files that are no longer available from Reactome.org to download (a denormalized version of the database, according to the doc, on 2010, but that might be inaccurate). Please see the following thread by Willem (the maintainer of reactome.db):