[go] contributes_to question

[Chris Mungall]

..which like many such recommendations will be ignored by the  
majority of implementations (in this case it is forgivable if we  
issue the recommendation at this late stage..)

Perhaps any association qualified in any way should be omitted from  
the default annotations we provide. We would of course also provide  
the full annotation set but it would be made obvious that this  
'advanced' set came with certain caveats

On Aug 14, 2007, at 8:00 AM, Midori Harris wrote:

> Whatever we decide, I would recommend that computational analyses  
> omit 'contributes_to' annotations.
>
> m
>
> On Mon, 13 Aug 2007, Valerie Wood wrote:
>
>> Recently I'm wondering recently why we have 2 meanings for  
>> contributes_to:
>>
>> When the qualifier was initially implemented, it was so function  
>> terms could be added to complexes like DNA polymerase and the F1  
>> Fo ATPase where the function cannot be attributed to a single  
>> subunit. This seems fine.
>>
>> Increasingly I see annotations to complexes which are described as  
>> (for example) a histone acetyltransferase complex, and all of the  
>> subunits are given histone de/acetlytransferase or  
>> methyltransferase activity with contributes_to, even thought the  
>> other subunits clearly have other functions (I see ATPases,  
>> ubiquitin ligases actin-like proteins etc, which are commonly  
>> associated with histone acetyltransferases and methyltransferases).
>>
>> This seems odd, for a number of reasons.
>> Often these subunits are not required for the activity, but their  
>> deletion (sometimes, but not always) affects the rate  the activity
>>
>> Primarily I don't understand what this type of 'contributes_to'  
>> annotation provides  to GO users above a process annotation to the  
>> histone acetylation (if this has been shown), a complex  
>> annotation, and a function term to unknown/root node.  Isn't it  
>> more useful to know that there is some information about the  
>> process, but the molecular function is not known?
>>
>> 1) Another problem is that these particular chromatin associated  
>> complexes often have shared subunits so the function annotations  
>> aren't so clear-cut (i.e some of these subunits may be members of  
>> other complexes which do not have this activity)
>>
>> 2) Also computational analysis using RCA which infer these  
>> 'functions' to similar proteins which, from their domain  
>> composition it is unlikely possess this activity. 3) It makes  
>> cross species comparisons difficult because you get different  
>> numbers of functions to what you would  expect when comparing  
>> annotations between species. For example it is known how many  
>> histone acetyltransferases /methytrasferases etc. pombe has,  
>> compered to S. cerevisiae, but when I compare the 2 the numbers  
>> are skewed.
>>
>> The documentation clearly allows this (although there is not an  
>> example of this type of annotation in the documentation, so I  
>> wonder if this is what we meant?):
>>
>>> From the documentation:
>>
>>
>> Annotating individual gene products according to attributes of a  
>> complex is especially useful for molecular function annotations in  
>> cases where a complex has an activity, but not all of the  
>> individual subunits do. (For example, there may be a known  
>> catalytic subunit and one or more additional subunits, or the  
>> activity may only be present when the complex is assembled.)  
>> Molecular function annotations of complex subunits that are not  
>> known to possess the activity of the complex must include the  
>> entry contributes_to in the Qualifier column.
>>
>> Note that contributes_to is not needed to annotate a catalytic  
>> subunit. Furthermore, contributes_to may be used for any non- 
>> catalytic subunit, whether the subunit is essential for the  
>> activity of the complex or not.
>>
>>
>>
>