900 papers

The numbers: 6,200 annotations of 899 papers about 2,306 proteins (58% of the genome)

So, it is done. Factum est. All papers until and including 2008 about Mycobacterium tuberculosis proteins (modulo some microarray-only and two-dozen without informative abstract) are annotated in GAF format. To achieve the last step, the correct format, I learned ruby and patched the bioruby package on the fly, which was fun---so I guess I stay with ruby (and bioruby) for some time.

Instead of doing The Right Thing[tm] now, which is quality control of the annotations, I'm thinking about fixing the GO parsing in bioruby. Guess what it will be.

Dduh

That's what I get for not researching thoroughly: the software isn't necessary because UniProt provides all annotations in GAF format. As this is text and one record per line, a simple grep does the trick. But it's even more embarrassing for the project leads, as the data is provided by UniProt just for those people that are part of an annotation project.

So, after additionally having provided them with a list of unannotated genes, let's see how it comes out.