Hi

Is there any sample scripts for creating AnnotationData Packages (like KEGG.db or GO.db) ?

I'm trying to create AnnotationData Package for http://kanaya.naist.jp/KNApSAcK/ .

Unfortunately, no. The scripts that we use to generate the 'higher level' databases (KEGG, GO, the db0 packages, etc) are primarily bash scripts that download lots of data from various sources and parse out the necessary data. As you can imagine these are fairly fragile, as the annotation services tend to change the format of their data files on a semi-regular basis, and being bash scripts are not necessarily portable. Running these scripts tends to be an iterative process where you fire them off, then when they break you have to track down what the problem is, and then run again.

The project is really going in the direction of getting most annotation into the AnnotationHub, so you will probably get better traction lobbying for these data to be added to AnnotationHub. Can you explain why people would want to use these data, and what the use cases are?

The alternative is to just download the standalone version and use it as the original developers intended. That seems like the easiest thing to do.