[Go] [Fwd: [Fwd: Re: [Annotation] annotating ribosomal proteins]]

[Judith Blake]

Hi Val,

There are many things in the works of functions for complexes and as you know this has been an issue for many years.  Currently, I don't think function gets assigned to members from assignement to the complex.  That's where the 'contributes to' comes in.  Some members of the complex, that have functionality (typically the catalytic unit) would be assigned the function; the other (typically structural) members of the complex would 'contribute_to' the function.

For S.pombe, check Gaa1....

CC - GP1-anchor transamidase complex
MF - (contributes_to) GP1 - anchor transamidase activity

Although there have been recent discussions about this.

RefGenome Feb10 call

Discussed use of 'colocalizes with' and 'contributes to'; there are two meanings for each and that is confusing. This is important because in both cases, one of the meanings is 'weaker' and can probably not be used for propagation. Pascale will send to every group the annotations they have using those qualifiers.

Contributes_to

    * Used with two different meanings: (1) when a multisubunit complex needs two or more gene products for activity, and (2) from documentation: "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." [1]
    * This last statement should be removed. It's incorrect to annotate a function as if annotating a component.
    * contributes_to for RG genes (txt); Image:Contributes to RG-2009-02.xls (xls)as of Feb 9, 2009:
    * Harold: this should be used only when it's absolutely required
    * sometimes get confused with regulation
    * Doug: should we carry the contributes_to when doing ISS?
    * Harold: for EXP: it depends on the experiment that was done

[ACTION ITEM]: fix documentation

Judy


On 3/2/09 9:16 AM, "Valerie Wood" <val at sanger.ac.uk> wrote:

This was the e-mail from keseler at ai.sri.com.
There may be other outstanding items on this list as I don't think
anybody  is responsible for checking thst items are resolved on here.

---------------------

Hi,

I don't think I can contribute anything but more questions to this
discussion, but would really like to know the answers.  First of all, I
could absolutely swear that not too long ago, I saw a sentence somewhere
in the annotation documentation saying something along the lines of, if
a complex has a function, the function is transferred to its subunits.
(Maybe it was about process, I don't recall.)  However, I can not find
this anywhere any more.  It is very important to us to know the answer
to this; in EcoCyc, I have the ability to annotate complexes themselves
with GO terms, and I think those become attached to the individual gene
products for the mapping file.

While poking around in the guide, I only found a couple of relevant
references to protein complexes.  Under "Valid Function Terms" in
http://geneontology.org/GO.function.guidelines.shtml, it says this:
"Functions are not restricted to the activities of single gene products;
multi-gene product complexes can also have functions."  That's generous
:-) , but no word on how to transfer those functions to single gene
products.  There is also a section on "Function Terms for Subunits",
which refers to the GO annotation guide for advice on how to annotate
subunits of a complex - in this case, referring to itself is not
entirely useful.

 From the discussion so far, my take-home message was that one should
never annotate components of a complex to a process or function of the
complex with IDA.  Is this the correct impression?  If yes, then looking
at this the other way, any function/process that is performed by a
multi-subunit complex will never have an IDA annotation.  No more IDAs
for translation, replication, transcription,...?

Aside from my IDA concerns, would it be possible to use IMP?  Granted,
if the mutant phenotype is death, that's not very interesting (Botstein
said so himself) nor very informative in and of itself, but if a protein
is part of the ribosome and you can't knock out the gene without killing
the cell, would it be a safe assumption that said subunit is involved in
translation?  (I think there *are* non-essential ribosomal subunits,
which would then not get the translation term.)

-Ingrid



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