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question about evidence codes

Midori Harris midori at ebi.ac.uk
Wed Sep 12 08:18:31 PDT 2001


Hi,

This is a good question! At the moment we don't have a good way to capture
something quite this subtle. I would recommend erring on the side of not
losing information, even though neither of the single pieces of evidence
is truly sufficient. GO annotations aren't meant to substitute for reading
the papers if one really wants to understand what's going on!

I suppose you could also argue that the IGI evidence alone tells you that
aub has a role in pole cell formation; it's unspecific in the sense of not
distinguishing between direct and indirect roles but isn't actually wrong
even without the second line of evidence.

Midori

On Wed, 12 Sep 2001, Gillian Millburn wrote:

> hello GO people,
> 
> I am trying to add a GO process term to my curation of a paper for
> FlyBase and I need some help.
> 
> The paper is:
> 
> Harris et al., 2001, Development 128(14): 2823--2832
> 
> which is about the aubergine (aub) gene.
> 
> The GO term I want to add is:
> 
> pole cell formation ; GO:0007279
> 
> but I am not sure what evidence code to add because of the way the
> experiment was done - they couldn't just look directly at pole cell
> formation in aub single mutants, because aub is required for efficient
> osk translation and osk itself is needed for pole cell formation, so
> the lack of pole cells in aub single mutants could be indirect due to
> its effect on osk translation.
> 
> The experiment they did was to overexpress the oskar (osk) gene in the
> anterior of embryos in an otherwise wild-type background and you get
> ectopic pole cells at the anterior of the embryo (as well as the normal
> ones at the posterior end).
> 
> They then make the embryos that are expressing osk anteriorly also
> mutant for aub and in these double mutant embryos they find that the
> ectopic pole cells are not formed.  This gives evidence that aub is
> required for the development of ectopic pole cells at the anterior of
> the embryo (evidence 1, IGI).
> 
> They also showed by using a UAS-GFP-aub transgene that aub is a
> component of the polar granules (evidence 2, IEP)
> 
> The two evidences combined I think give enough evidence that aub is
> involved in formation of the (normal) posterior pole cells, but I don't
> think that either evidence alone is enough to add the GO term above to
> the aub gene.
> 
> There is a bit in the GO evidence documentation which suggests I should
> use TAS:
> 
> > Added 2000-11-08: Heather has seen cases where a paper presents
> > several lines of evidence supporting a conclusion, of which each line
> > of evidence alone is sufficient to annotate to a higher-level (more
> > genric) node, but combining the lines of evidence gives the author (or
> > curator) enough data to support annotating to a lower-level (more
> > specific) node. We've decided to annotate each line of evidence
> > singly, with the appropriate evidence code, for the higher node
> > (e.g. have a line for IMP, another line for IPI, for one GO ID). The
> > annotation to the lower node can then be included with 'TAS' as the
> > evidence; cite the paper if the author draws the conclusion. If the
> > curator draws the conclusion, keep some record of what went into the
> > decision.
> 
> 
> so I could add:
> 
> pole cell formation ; GO:0007279 | TAS
> 
> but in this case there isn't really a higer level (more general) term I
> could add with the IGI or IEP evidences. If I only put the above line I
> will lose information.
> 
> Could you clarify whether if a GO term is added with a single piece of
> evidence, e.g.:
> 
> pole cell formation ; GO:0007279 | IGI with FB:osk
> pole cell formation ; GO:0007279 | IEP
> 
> that the implication is that the single type of evidence alone is
> enough to assign the GO term - if that is the case then I cannot add
> the above 2 GO terms to aub because I don't think its true - you need
> both of them combined, but if I don't put the above 2 GO terms and only
> put the TAS one then I lose info, help !!
> 
> Gillian
> 
> --------------------------------------------------------------
> Gillian Millburn.
> 
> FlyBase (Cambridge),
> Department of Genetics,
> University of Cambridge,
> Downing Street,                       email: gm119 at gen.cam.ac.uk
> Cambridge,  CB2 3EH,                  Ph : 01223-333963
> UK.                                   FAX: 01223-333992
> --------------------------------------------------------------
> 
> 
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