[Annotation] annotating ribosomal proteins
Karen Christie
kchris at genome.stanford.edu
Wed Jun 18 11:25:29 PDT 2008
sure ;) SGD wouldn't mind. We're mostly done with all 138 or so of them,
and only a minority of ours have duplicated genes!
... probably not a good idea to do them all in one month
-Karen
On Wed, 18 Jun 2008, Pascale Gaudet wrote:
> On a related topic- should we take all ribosomal proteins as annotation targets for
> July?
>
> Karen Christie wrote:
> we're talking about the process annotations (and the contributes to
> qualifier is valid only for function) and which evidence code to use.
>
> -K
>
>
> On Wed, 18 Jun 2008, hjd at informatics.jax.org wrote:
>
> I would think the individual members of the complex would an a
> contribute_to qualifer for the activity term annotation, with
> each member
> having a component annotation to the complex. That way no one
> would be
> confused into thinking that the particuarl protein had the
> activity all by
> itself.
>
> hjd
>
>
> 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
>
> Valerie Wood wrote:
>
> I was thinking along the same lines, but
> that we could do IPI with
> GO:complexID
>
> I don't think we should use IDA. Up to
> now, where there is no direct
> evidence for the process, I have used IC
> from GO:complexID for the
> process if the inference can be made
> from an IDA to a complex, but
> this is probably not ideal.
>
> Val
>
> Midori Harris wrote:
> Reactome has identifiers for
> complexes ... could you use
> IPI with the
> Reactome ID for the
> ribosome? (E.g. S.
> cerevisiae ribosome is
> Reactome:141693; H. sapiens
> is 72500.)
>
> If this is a stupid idea,
> I'll bow out quietly ...
> it's been a long,
> long time since I did
> annotation.
>
> m
>
> On Tue, 17 Jun 2008, Karen
> Christie wrote:
>
> As of the 2006
> Annotation camp,
> we agreed that
> IPI could only
> be
> used when you
> know it is a
> direct
> interaction and
> that you should
> fill the with
> column with the
> directly
> interacting gene
> products.
>
> Prior to that, I
> often used to
> use IPI for the
> proteins that
> came
> down in a
> complex, and for
> 'modern'
> purifications
> where one
> protein
> was tagged, I'd
> put that one in
> the with column.
> But we agreed
> that
> it isn't known
> that this is
> direct, so we
> quit doing it.
> I've been
> having the same
> problem with
> spliceosomal
> complexes and
> have become
> rather unkeen on
> the decision
> that IPI could
> only be used for
> known
> direct
> interactions. It
> seems that this
> requirement got
> added by the
> people who want
> to use the IPI
> with field as a
> protein-protein
> interaction
> database.
>
> Anyway, I
> thought that IPI
> with the tagged
> protein seemed
> like a
> much better
> representation
> of the evidence
> for the process
> than IDA.
> Coming down as
> part of a
> complex doesn't
> seem like a
> direct assay
> for process. IPI
> with one of the
> proteins in the
> complex seems
> like
> a better
> representation
> of what was
> actually done,
> but we can't do
> now that because
> of the direct
> interaction
> requirement.
>
> IC also seems a
> little
> unsatisfying,
> since it's not
> experimental. I
> don't know,
> maybe for
> complexes as
> well
> characterized as
> the
> ribosome, or the
> spliceosome,
> just being in
> the complex is
> direct
> evidence that
> it's part of the
> process that the
> complex is
> experimentally
> characterized to
> be part of...
>
> I've been a bit
> muddled about
> how best to deal
> with these ever
> since
> the 2006
> Annotation camp.
> I liked using
> IPI better than
> IDA...
>
> -Karen
>
>
> On Tue, 17 Jun
> 2008, Pascale
> Gaudet wrote:
>
> Can
> you
> then
> IPI
> the
> process?
>
> Doug
> howe
> wrote:
>
> I
> think:
>
> "the
> IDA
> is
> just
> for
> the
> annotation
> to
> the
> complex
> term
> and
> then
> use
> IC
> from
> the
>
> complex
> term
> for
> the
> Process
> annotation"
>
> is
> the
> way
> to
> go.
>
>
> Doug
>
>
> Karen
> Christie
> wrote:
>
> Hi
> Pascale,
>
>
> Rama
> is
> looking
> at
> the
> original
> papers,
> and
> ribosomes
> and
> the
> processes
>
> of
> ribosome
> assembly
> are
> probably
> better
> characterized
> in
> cerevisiae
>
> than
> in
> any
> other
> eukaryote.
>
>
> The
> real
> issue
> here
> is
> that
> what
> has
> been
> shown
> is
> that
> protein
> X is
>
> part
> of a
> big
> complex,
> e.g.
> the
> ribosome,
> for
> which
> the
> function
> is
>
> known.
> The
> sum
> total
> of
> the
> experimental
> evidence
> available
> for
> a
>
> significant
> number
> of
> ribosomal
> proteins
> is
> that
> they
> are
> purified
> as
>
> part
> of
> the
> ribosome
> complex.
> So,
> for
> component,
> it's
> easy.
> This
> is
> IDA
>
> evidence
> that
> protein
> X is
> in
> the
> ribosome,
> or
> in
> the
> Small
> SubUnit
>
> (SSU)
> or
> in
> the
> Large
> SubUnit
> (LSU),
> or
> whatever
> complex
> is
>
> characterized.
>
>
> But
> is
> being
> in
> the
> ribosome
> considered
> to
> be
> IDA
> evidence
> for
> a
> process
>
> annotation
> to
> translation?
> In
> one
> way
> of
> looking
> at
> it,
> the
> direct
> assay
>
> is
> that
> it's
> part
> of a
> complex
> and
> then
> you're
> assuming
> that
> the
>
> individual
> protein
> is
> involved
> in
> translation
> because
> it's
> in
> that
>
> complex.
> Is
> this
> a
> direct
> assay
> for
> being
> involved
> in
> translation?
> Can
>
> we
> use
> IDA
> for
> a
> process
> annotation?
> or
> is
> it a
> more
> accurate
> statement
>
> to
> say
> that
> the
> IDA
> is
> just
> for
> the
> annotation
> to
> the
> complex
> term
> and
>
> then
> use
> IC
> from
> the
> complex
> term
> for
> the
> Process
> annotation?
>
>
> -Karen
>
>
>
>
> On
> Tue,
> 17
> Jun
> 2008,
> Pascale
> Gaudet
> wrote:
>
>
> Hi
> Rama,
>
>
> I
> think
> this
> is a
> perfect
> case
> where
> one
> of
> us
> should
> go
>
> back
> to
> the
> original
> papers
> and
> find
>
> what
> we
> all
> need
> to
> ISS
> to
> (in
> which
> organism
> the
> funtion
>
> and
> process
> were
> shown).
>
>
> Pascale
>
>
> Rama
> Balakrishnan
> wrote:
>
> Hi,
>
>
> I
> have
> couple
> of
> ribosomal
> proteins
> to
> annotate
> as
>
> part
> of
> the
> ref-genome
> curation
>
> project.
> Turns
> out
> that
> there
> is
> no
> direct
>
> experimental
> evidence
> showing
> that
> these
>
> proteins
> are
> involved
> in
> translation.
> Almost
> all
> the
>
> studies
> purify
> the
> ribosome
>
> from
> yeast
> and
> identify
> the
> subunits
> by
> one
> or
> more
>
> techniques.
>
>
> I
> can
> do
> IDA
> for
> CC
> annotation,
> that
> is
>
> straightforward.
> Is
> IDA
> for
> function
>
> annotation-
> structural
> constituent
> of
> ribsomome
> okay?
>
> What
> about
> BP?
> I
> can
> do
> IC
>
> from
> the
> CC
> term,
> but
> that
> is
> not
> direct
> experimental
>
> evidence.
> What
> do
> you
> all
>
> think?
>
>
> Thanks
> for
> your
> time,
>
>
> Rama
>
>
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