[go] contributes_to question

[Valerie Wood]

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.


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