It may be a little more complicated than a GUI fix - I've been looking at the
code in view_experiment.jsp and it's basically this (much simplified [by
removing all null checks]):
for (RawBioAssay item : rawBioAssays)
{
AnnotationSet as = item.getAnnotationSet();
for (AnnotationType at : experimentalFactors)
{
List<?> factorValues = as.findAnnotation(at).getValues();
/* display factorValues */
}
}
I haven't yet figured out how inherited annotations are handled in the API,
but somehow I think that item.getAnnotationSet() ought to be returning some
kind of merged AnnotationSet (based on two samples' AnnotationSets in this
case), however this nearby line of code suggests that an AnnotationSet can
only have one associated Item.
aItem = a.getAnnotationSet().getItem();
I need to read up more on inherited annotations before commenting further (and
this won't be today) - I just think the GUI code looks OK to me.
cheers,
Bob.
Nicklas Nordborg writes:
> Dominic Oyeniran wrote:
> > Nicklas Nordborg wrote:
> >> Dominic Oyeniran wrote:
> >>> Hi Micha,
> >>>
> >>> Micha Bayer wrote:
> >>>> Hi Dominic,
> >>>>
> >>>> We are trying to export our first experiment for real so we can submit
> >>>> it to ArrayExpress, and initially it looked like everything had worked
> >>>> okay. But now we have found an error with the annotation that I wanted
> >>>> to ask you about.
> >>>> Our experiment is a two-colour one, and we have a factor which can take
> >>>> the value of mutant or wildtype. Both mutant and wildtype sample is
> >>>> applied to the hybridization (one per channel) and we then want the
> >>>> RawBioAssay item to inherit its annotations. The only way we could find
> >>>> to do that was to inherit from both the samples, but then only one of
> >>>> them is exported into the tab2mage file, which presumably is not good
> >>>> enough for ArrayExpress.
> >>> This is becuase BASE chooses the first of the inherited annotations
> >>> values that it finds for sample, assigns and displays this as the factor
> >>> value for the experiment.
> >> BASE doesn't choose one of them. All inherited annotation values are
> >> always displayed.
> >>
> >
> >
> > BASE actually chooses one of them, at least as shown on the GUI here.
> > It's not the exprimental factors section of the GUI parse that's
> > relevant here, based on my understanding, but the Raw Bio assays section
> > listing each raw bio assay included in the experiment. Since
> > experimental factor values/annotation values has to be propagated
> > through the Raw Bio assays.
> >
> > For each Raw Bio assay in an experiment, you can only see or get one of
> > the inherited values having inherited annotations from two different
> > Sample items each from a line in the two channel hyb.
> >
> > However, the inherited values are displayed as separate annotations for
> > the raw bio assays on the 'Inherited annotations and protocol parameters
> > section' of the view page.
> >
> > If this is not the case then I must have a wrong understanding of how
> > factor values annotation are obtained or handled in BASE.
>
> It actually seems like the GUI only displays one of the inherited
> annotations on the Experiments page. This should of course be corrected
> to display all annotations. Note that this is just a display problem.
> All the inherited annotations are stored in the database and can be
> viewed from the Raw Bioassay page which doesn't have this bug.
>
> If the Tab2Mage exporter has the same problem, it has to be corrected in
> it's code as well.
>
> /Nicklas
>
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--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
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