M.tb. sulfur metabolism at reactome

Not the whole sulfur, but assimilation and cysteine biosynthesis pathways are now at reactome, and a picture too. So, what's next? On the human side, I'll tackle MoCo biosynthesis. On the bacillus, maybe look at which processes have most functional annotations and start from there?

Wow, quality control quite involved me again with programming, and prototyping with ruby is really fast. What takes time at this moment of learning a new language is the unexpected language details (say quirks), and of course, OO design. So, most quality rules I know of are applied. I'm now waiting for marks from the EBI GOA group, and further rules to apply. This means, yes, both the Indians and the EBI got the data now, as planned. Meanwhile, stalled work on M.tb pathways in reactome format continues.

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.

just had to comment on an article from the 2009 Hindustan Times with an interesting story: an Indian expat wants to reestablish himself in his birth country. First thing he does, he writes a report and tries to capitalize all science assets he finds---without syncing with any political peers. Consequently, he is frowned upon and loses his job. Last I saw was his blog spewing one-sided information at his previous employer-to-be. Now, what does this tell the reader? First, before returning "home", check political compatibility; if not matching, first find peers with power before embarking on touchy subjects. It also proves having a standard scientific education does not create political sensibility in a person.

600 papers, 3700 annotations on 1600 genes!

reaction

not totally unexpectedly, something has boiled over, and in Nature as that, no less. This online article gives some people voice who were not amused by some too early announcements (we wrote about that too). And no wonder the publishing houses grab any opportunity to discredit efforts that might make them obsolete if succesful. On the other hand, it could be an opportunity to win more moral ground by pointing at those that didn't participate. So, let's look at the interesting bits.

Nature writes Brahmachari's highly publicized announcement on 11 April that the project has comprehensively mapped, compiled and verified the genome of M.tb. but they don't give any reference to Brahmachari's alleged announcement. They would be hard pressed. It was all Indian mass media quoting Brahmachari and I give him the benefit of the doubt that he was misquoted. I mean, not even the author of the Nature comment appears to have a grasp about what the first phase of TBGO was about.

As we read on, however, clouds accumulate. Brahmachari was misquoted another time? It depends on how succesful Raghava was with his neural nets. Probably he had some result, and that was overhyped by Brahmachari. I can now see that.

Next, a description of the TBGO sub project contains a link to some completely different thing on TBrowse, and Jayaraman doesn't notice it. Talk about quality paper. But Gohkale, the CSIR director, has no clue either. He apparently wasn't told that "the data" is still not available, the effort of the few dozen remaining participants is stalling, and no one does any real work except that bloody fool from Berlin who single-handedly annotates all 7-800 papers on the subject, and doesn't see a single rupee of the cake!

The rest of the article is opinions.

In my opinion, the real issue is not that some unlucky people frantically try to make the best of a seemingly hopeless situation (you mean bloody students?) and a whopping $32 million. I would never stay in the path of people with such visions. I would rather finish annotating (July), then write my part of the paper, and quietly switch to pathway work at reactome.org. I can guess, however, that there will be more on the subject, if not from the frightened houses.

milestones

today quite an important milestone passed: my private GO annotations for M. tuberculosis reached 500 annotated papers. It is important because that was the rough number I projected first from my starting impression. However, 50 more are in the queue, and the final sweep still not done. So it could easily become 700. As to the other numbers, we have altogether 1950 annotations on 650 gene products, that is 15 per cent of the genome.

The "genome map" is released! What? Ah, the ontology annotations were announced. The most informative take is at livemint and -- hold it, it says CSIR to unveil gene map (at www.osdd.net) -- so, no, not much really happened except that we know now that to-be-published annotations can be edited Wikipedia-style later. I'm quite sure, however, that most genes already have some annotation now in the putative official version.

I'll grab the opportunity to publish data about my private annotation effort which is about halfway through. I have looked at 350 papers of which 240 are now annotated, yielding 810 annotations of 350 gene products. Not even ten percent of the genome.