[go] Paper of potential interest to you

[David Hill]

Yes, my take on this paper was that the biggest thing it showed was that 
we need more curators!

Valerie Wood wrote:
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> 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.
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> camon at ebi.ac.uk wrote:
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>> 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
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>>> Mike Cherry wrote:
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>>>   
>>>> 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.
>>>
>>>   
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