[go] contributes_to question
Susan Tweedie
sart2 at gen.cam.ac.uk
Thu Aug 16 06:01:42 PDT 2007
Hi Val
On Thu, 2007-08-16 at 13:19 +0100, Valerie Wood wrote:
> It seems we have all used it slightly differently anyway.
> 2.
> FET3/YMR058W
> is a copper oxidate involved in iron assimilation by reduction and
> transport. it isn't a transporter but it is part of the transporter complex.
>
> This has an iron transporter activity (with contributes to) in SGD, and
> has been ISS's to this activity (without contributes_to) by two
> drosophila genes (FBgn0032116 and FBgn0039387)
Thanks for pointing these out. I'll review these old ISS annotations for
FBgn0032116 and FBgn0039387. In general, we shouldn't drop the
'contributes_to' when making an ISS.
I'll also have a look at our 'contributes_to' annotations to see how
consistent we have been. I've used it fairly sparingly for essential
subunits of an activity.
Susan
> I see man many examples of this (too many to give feedback on)
>
> Can this go on the agenda for September meeting?
>
> Val
>
>
>
>
>
> Pascale Gaudet wrote:
>
> > I did mean unessential role; ie, the complex might have the activity
> > without the protein you're annotating, but adding it enhances the
> > activity (but not a regulator-- that would be 'positive regulation
> > of...'). But if adding it does nothing, I would annotate to unknown.
> >
> > Pascale
> >
> > Valerie Wood wrote:
> >
> >>It seems so to me too, these are equivalent to process annotations
> >>But did you mean essential role in the activity ? This is how I would use it.
> >>
> >>VAl
> >>
> >>
> >>Pascale Gaudet <pgaudet at northwestern.edu> wrote:
> >>
> >>
> >>><!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
> >>><html>
> >>><head>
> >>> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
> >>> <title></title>
> >>></head>
> >>><body bgcolor="#ffffff" text="#000000">
> >>>Val, <br>
> >>>My understanding was that the subunit had to have at least an
> >>>unessential role in the activity, although the documentation is very
> >>>ambiguous. But what you are describing is really capturing component
> >>>information with a function annotation. That seems wrong. <br>
> >>><br>
> >>>Pascale<br>
> >>><br>
> >>><br>
> >>>Valerie Wood wrote:
> >>><blockquote cite="mid:E1ILDTY-0006f2-Vx at web-2-10.internal.sanger.ac.uk"
> >>> type="cite">
> >>> <pre wrap="">I'm really asking the question why arbitrarily add these function annotations to the 'unknown' subunits
> >>>of complexes in the first place, when they are clearly not the subunit that posseses the catalytic activity, or when they clearly have another activity.
> >>>
> >>>Some of these complexes have
> >>>ATPase activity,
> >>>ubiquitin ligase activity
> >>>acetyltransferase activity
> >>>etc.
> >>>
> >>>so if this type of annotation was valid (or useful) then we would (presumably) add all these annotations to all subunits for completion?
> >>>
> >>>Wouldn't users rather see which subunits had known function and which had 'unknown function'.
> >>>It just seems that the qualifier is being used much more liberally than was originally intended (i.e as a filler to avoid adding an 'unknown' annotation)
> >>>
> >>>and it skews functional predictions/genome comparisons.
> >>>
> >>>
> >>>val
> >>>
> >>>
> >>>
> >>>
> >>>Chris Mungall <a class="moz-txt-link-rfc2396E" href="mailto:cjm at fruitfly.org"><cjm at fruitfly.org></a> wrote:
> >>> </pre>
> >>> <blockquote type="cite">
> >>> <pre wrap="">..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:
> >>>
> >>> </pre>
> >>> <blockquote type="cite">
> >>> <pre wrap="">Whatever we decide, I would recommend that computational analyses
> >>>omit 'contributes_to' annotations.
> >>>
> >>>m
> >>>
> >>>On Mon, 13 Aug 2007, Valerie Wood wrote:
> >>>
> >>> </pre>
> >>> <blockquote type="cite">
> >>> <pre wrap="">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?):
> >>>
> >>> </pre>
> >>> <blockquote type="cite">
> >>> <pre wrap="">From the documentation:
> >>> </pre>
> >>> </blockquote>
> >>> <pre wrap="">
> >>>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.
> >>>
> >>>
> >>>
> >>> </pre>
> >>> </blockquote>
> >>> </blockquote>
> >>> </blockquote>
> >>> <pre wrap=""><!---->
> >>> </pre>
> >>></blockquote>
> >>></body>
> >>></html>
> >>>
> >>>
> >>>
> >>
> >>
> >>
>
>
>
More information about the Go
mailing list