Nautilus

Incentives needed for genome annotation

Roy Welch and Laura Welch of Syracuse University, New York, examine why researchers seem reluctant to be more directly involved in the annotation of microbial genomes in the February issue of Nature Reviews Microbiology (7, 90; 2009). They write:

“To annotate an organism’s genome, biological information about the organism must be matched to the genes and genetic elements in the sequenced genome. The process is iterative and open-ended: new information is constantly incorporated into the annotation. It can also be recursive: analysis of the annotation may provide insight about the organism that in turn leads to changes to the annotation. Unfortunately, the generation of new information and annotation of the genome are at present completely separate processes. Often new information does not become incorporated into the annotation in a timely manner, a costly loss for those who rely on it to advance their research.

The community of expert researchers who study an organism produce most of the information that becomes part of the annotation and are also the primary group of end-users. It is therefore curious that the annotation process is circuitous and inefficient: researchers communicate new information not as direct updates to the annotation, but as research papers that must later be interpreted and incorporated into the annotation separately — most often by a third party! Indeed, some information never finds its way into the annotation. It would be far more efficient for the research community to contribute directly to genome annotation. Yet the life science community as a whole remains stuck in the old, inefficient paradigm.”

The authors go on to argue that technology is not the impediment, given the wide availability of wikis (collaborative editing websites) and the databases that have been created using these technologies, including EcoliWiki, GONUTS, Myxopedia and Wikipathways. Rather, state the authors, the impediment seems to be sociological: until contributions to a genome-annotation collaborative information repository can be credited by inclusion in a PhD thesis, curriculum vitae, tenure application or grant proposal, direct collaborative annotations are unlikely to fulfil their promise and potential to accelerate scientific achievement.

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