Friday, June 19, 2009

New genome article added to 'PLoS ONE prokaryotic genome collection'

The article presents most important observations such as those related to the presence of several novel virulence determinants of non-mycobacterial origins and that these were perhaps acquired from other environmental organisms and pathogens including Rhodococcus sp., Streptomyces sp., pseudomonads and Burkholderia cepacia.

Standards for genome data reporting: should we go about it?

Within my overview article that accompanies the PLoS ONE Prokaryotic Genome Collection, one thing that I did not touch base with was the standards for genome data reporting. The Genome Standards Consortium (GSC) is now already in place (and I am one proud member of the same!) and they strongly advocate that certain standards be introduced (at the least) at the level of genome meta data. The consortium has recently published aims and objectives, prospective guidelines and envisaged benefits of such 'would be' mandatory standards (http://www.pubmedcentral....).

As a next critical step, the GSC are now starting to ask journals to require that new genome/metagenome publications be accompanied by completed 'Minumum Information about a Genome Sequence (MIGS/MIMS)' reports.

This sounds a wonderful proposition and I guess PLoS journals in this connection could lead headway as they already insist for adherence to certain other standards such as MIAME for reporting microarray data). Until this point, it is all OK. But some people feel that 'monopolizing' standards could be a kind of 'suffocation'. However, I am sure this will not lead to the kind of 'suffocating monopoly' created by certain 'nomenclature commissions' and their 'mouthpiece journals' in the area of taxonomy and systematics.

I discussed this with one of my friend, a genomic/bioinformatics expert and he says ".. my problem with standards is also not only the monopoly, but that it is also really hard to set a minimal role of meta data that need to be entered per genome. I suffer from the lack of organized meta data; but once the entry is enforced, people will just start putting anything to fill the tables and get their data out, which will lead to the opposite of what standards are supposed to achieve".

Given above, it is clear that some discussion and brainstorming is nevertheless required before journals start insisting for the MIGS/MIMS reports. I can not find a better place than PLoS ONE (sandbox) to discuss and resolve such issues.