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.

a big sigh

There's a saying by Bismarck: "The 1st generation creates value, the 2nd manages it, the 3rd studies art history, the 4th degenerates." I would like to state a version regarding computer science: "The 1st generation creates algorithms, the 2nd writes and patches app software, the 3rd merely knows how to download and install safely, the 4th blindly believes in computer power." OTOH, there have been people who started at four and made it to position one, all in one person, so don't take the saying as a prediction of the future, although sometimes it looks like it.

Having made my big sigh, I'm now (the?) one who makes GO annotations from the literature on mycobacterial (as in tuberculosis) protein function. I intend to do a complete job, even if I'm not the only one, because I know my level of quality, and comparing two version will give a better one. This will take two three months. After that, let's hope someone has written the software we need...