Thanks for that Nicklas, I had only checked out the overview feature briefly
once before. It's very powerful (being able to disable certain warnings is
nice). And the Properties tab of the experiment page does indeed list the
inherited annotations for each experimental factor - it would be pretty easy
spot a missing one!
Just a general comment... BASE2 is really really nice! Having mainly used
Genepix in BASE1, I just installed the Affymetrix plugins for BASE2 and found
that it all worked first time. The project feature is excellent.
cheers,
Bob.
Nicklas Nordborg writes:
Bob MacCallum wrote:
A useful GUI addition would be another column on the Raw bioassays
list view called 'Has inherited annotations'. The content of that column
would be a simple yes/no. Alternatively, it could be called 'Inherited
annotations' and could provide more information.
Without this I don't see an efficient way to check that I have remembered
to inherit annotations for each raw bioassay.
Assuming that you have put the raw bioassays in an experiment, and that
you have set the selected the annotation types you are interested in as
experimental factors, this will show up on the experiment page
(Properties tab).
Another way is to go to the Overview tab. This will list everything in
the experiment in a tree-like structure up to biosources and array
designs. It will also check that you have values for all experimental
factors and a lot of other things. If something is missing or incorrect
there are links that take you directly to a form for fixing it. Read
more about this in the user documentation:
http://base.thep.lu.se/chrome/site/doc/html/userdoc/analysis/experiments_analysis.experiments.html#experiments_analysis.experiment.overview
Obviously this would be suitable for other item types too.
It might even be nice to be able to set up default annotation
inheritance paths for a Project, but that's probably a bigger task.
I think there is need for a better interface for inheriting annotations.
or a smart way to make it happen automatically. As it is now the system
is a bit cumbersome to use. But I really don't have any ideas how to
make things better so any thoughts are welcome.
A related aside:
So correct me if I'm wrong, but it seems that for most purposes, you only
need to inherit annotations from Sample or Biosource to Raw bioassays.
Although you can inherit these annotations at each intermediate step
(extract, labelled extract, hyb, scan), the last step is the important
one
(for analysis).
Yes, it doesn't make much sense to inherit annotations to anything else
than raw bioassays. This is the only place where they are used by BASE.
When analyzing only annotations from raw bioassays, bioassay sets and
bioassays can be used.
/Nicklas
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Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
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