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question about evidence codes

Gillian Millburn (Genetics) gm119 at gen.cam.ac.uk
Wed Sep 12 05:52:32 PDT 2001


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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