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question about evidence codes

Gillian Millburn (Genetics) gm119 at gen.cam.ac.uk
Wed Sep 12 08:29:28 PDT 2001


Hi Midori,

> 
> 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.

yeah I wondered about this.

I will add 

pole cell formation ; GO:0007279 | TAS
pole cell formation ; GO:0007279 | IGI with FB:osk
pole cell formation ; GO:0007279 | IEP

and stick something in internal notes in case anyone wonders in the
future why I put all 3 evidences in !

Gillian

> 
> 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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> 
> 
> 


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