[Annotation] [Fwd: HIGH level GO mapping]

[Valerie Wood]

Hi Emily,

I suggested to David that these should probably not be mapped to 
molecular function root node (I think there are some IEA root terms 
mappings already, but I filter and discard them for pombe, on the basis 
that all root node annotation should be manually curated). For most of 
these IEA root node annotations, even though there is not a general 
mapping which can be added  more specific annotations can be/are made, 
so the root node annotations are confusing.

In general, a root node annotation means that there is no information on 
the F,P,C for the gene in question (albeit with ND). What the IEA 
mapping to the root node is saying is that no generic IEA mapping can be 
identified, which is slightly different. I would prefer to see no 
mapping in these cases, reserving root node annotations for cases where 
there really is no data, but I don't know if there is a general 
consensus for this.

I raised this as a divergent issue on this list, thread
Re: [Annotation] check for ND + additional annotation
 09/05/08 10:43

Val


David Lonsdale wrote:
> Hi Emily,
>
> What is the policy on high level mapping in the absnce of other 
> available terms
> e.g.
> GO:0008150 - Biological process
> GO:0003674 - Molecular function
>
> The case of entry IPR000994 comes to mind. It represents the Peptidase 
> M24 fold. It was (is) named the 'Peptidase M24, catalytic core' ---- BUT
> and was mapped to peptidase activity.
>
> However, it has three basic functions:
> 1. protein binding
> 2. metal ion binding
> 3. hydrolase activity
>
> The entry contains :
> peptidases (1,2,3 - categories)
> creatinase  (1,3 - categories)
> Spt3 (Fact complex component) - ( 1 -category)
>
> Therefore it cannot be GO mapped to peptidase activity nor can it be 
> GO mapped to 'hydrolase activity' nor 'catalytic activity'; but above 
> that is 'molecualr function'. Can we map at that top level is the query.
>
> This is quite important as it will affect many entries that have an 
> SSF identifying a structural fold that is involved in some form of 
> catalytic activity.
>
> Look forward to your reponse.
>
> cheers David


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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
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