[go] Paper of potential interest to you

[Valerie Wood]

Yes it would be more interesting to see a paper which showed the number 
of papers read and the number of annotations made vs the number of 
curators (which I doubt has increased much over time). That would be 
more eye-opening :) I think most people assume that there is some sort 
of 'curation army' somewhere.






camon at ebi.ac.uk wrote:

>Hi Val,
>
>The GOA group ( and therefore UniProtKB) do not integrate ISS or IEA from
>other GOC members at the moment. UniProtKB/Swiss-Prot shows all manual GO
>annotation (minus ND), filtered by source, UniProtKB shows manual and IEA
>annotations.
>
>One of our colleagues made some comments on this paper:
>
>'the real question that need to be asked is if manual curation capable of
>keeping up with the growth in biological knowlege (not the growth in
>sequences).  If a curator annotates a protein in a model organism, or an
>InterPro family, or a protien with a novel function, they are doing so in
>the belief that they are making (at some level) a generic statement, not
>just annotating one of the billions of sequences that happen to exist. 
>Observing the continued existence of unannotated (and frequently,
>according to the current scientific knowlege, unannotable) things is of
>very little importance: what matters is how much real, transferrable
>knowledge is recorded in the databases.
>
>and they don't even consider that an annotation may or may not be correct,
>and may or may not be useful.  it would be easy to increase metrics of
>coverage by adding wrong and/or high level GO terms to every protein'
>
>It's a shame we were not contacted before publication, im not sure that
>these papers help the curation effort already hugely understaffed.
>
>Evelyn
>
>
>  
>
>>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.....
>>
>>
>>
>>
>>--
>>The Wellcome Trust Sanger Institute is operated by Genome Research
>>Limited, a charity registered in England with number 1021457 and a
>>company registered in England with number 2742969, whose registered
>>office is 215 Euston Road, London, NW1 2BE.
>>
>>    
>>
>
>
>
>  
>



-- 
The Wellcome Trust Sanger Institute is operated by Genome Research 
Limited, a charity registered in England with number 1021457 and a 
company registered in England with number 2742969, whose registered 
office is 215 Euston Road, London, NW1 2BE.