[go] Paper of potential interest to you

[Valerie Wood]

Mike Cherry wrote:

> Manual curation is not sufficient for annotation of genomic databases
> William A. Baumgartner, Jr, K. Bretonnel Cohen, Lynne M. Fox, George
> Acquaah-Mensah, and Lawrence Hunter
> Bioinformatics 2007 23: i41-i48.
>
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/ 
> i41?etoc
>
>
>


This was interesting. Before we all decide its a losing battle, it's not 
quite so doom and gloom as this analysis suggests.

By using mouse and fly they chose the 2 models with the single greatest 
volume of data. It would have been nice to see the combined progress of 
the GO curated organisms vs. non GO curated organisms (rather than 
mouse, fly and then the entire Uniprot knowledge base)

Using this criteria (at least one GO annotation) they would have 
identified a 'best case scenario' (left graph of figure one') for both 
budding and fission yeasts.

However, using these methods, they would never show a 'best case 
scenario' of GO annotation for ANY organism because they extracted the 
GO data from the Uniprot records (at least this is what they say in the 
methods), and Uniprot don't include ISS/IC/NAS/TAS/ or most importantly 
for this analysis ND (I think that is correct isn't it Emily?)

And as they mention one reviewer pointed out, it is impossible here to 
differentiate between a rate limiting factor of the rate of annotation 
and the rate of discovery, or the relative contributions of either.

As an evaluation of GO coverage it would have been more informative if 
they had used all the GO data. But its difficult to provide an analysis 
of curation completion unless you know what is known.....




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