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 > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
