[go] Paper of potential interest to you

[camon at ebi.ac.uk]

UniProtKB shows manual and IEA
> annotations.

I meant UniProtKB/Trembl shows manual and IEA GO annotations...

so yes GOC would have had more..

Evelyn


> 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.
>>
>
>
>