[Annotation] [Fwd: HIGH level GO mapping]

[edimmer at ebi.ac.uk]

Hi David, Val and Jennifer

Yes, I agree with Val.  If no more granualar term can be located than the
root terms, then am InterPro domain should not be mapped.

My interpretation of the annotation to the root terms is a little
different - which ever method is used - manual or electronic - all
annotations to root terms simply state that no detail of its MF, BP or CC
can be provided, and if the manual ND code is used, this indicates that no
data can be found by a curator, whereas if the InterPro2GO reference is
inserted, it means that no information can be provided using this method.
In any case! Our two interpretations come to the same conclusion, that
InterPro2GO mappings to such terms are unuseful to the user of the
annotation sets. They may be handy for curators of the mapping, but I
think we could look to having such information stored elsewhere :-)

Emily

> 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
>
>
> --
> ---------------------------------------------------------------------------
> Valerie Wood			 Tel: 01223 496909
> S. pombe Genome Project		 Fax: 01223 494919
> Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
> Wellcome Trust Genome Campus	 http://www.genedb.org/genedb/pombe
> Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe
>
>
>
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