Bob MacCallum wrote: > > > Also: the only reason I am trying to do things this way is because it > > > seems the only way to automate annotation of raw bioassays, but > > > technically they should really inherit their annotations from the > > > appropriate entity upstream (e.g. BioSources). Is there any means of > > > "batch-inheriting" annotations, without having to set them manually for > > > every bioassay in the experiment individually? Can't seem to find > > > anything in the docu regarding this. > > > > There is a new function in BASE 2.9 that can make this easier > > (http://base.thep.lu.se/ticket/1133). First, you need to put the raw > > bioassays in an experiment and select experimental factors (=annotation > > types) for it. > > > > When this has been done, you can access a function on the experiment's > > "Properties" page that automatically inherits all annotations for the > > experimental factors. After this you may want to check out the > > "Experiment overview" page to find annotations that have been inherited > > multiple times. This happens if there is more than one parent item that > > has annotation values for the same annotation type. > > For two colour designs, we usually only inherit from the "experimental" > biosource. (Explanation: an experimental samples might be annotated as > "Infected with E. coli", "Infected with S. aureus" and so on, and the control > samples would be annotated as "Mock infected with PBS".) > > It looks like the automatic inheritance will also inherit from the the > "control" biosource.
Yes, it will inherit all annotations that it can find, because it can't tell which ones are "important" and which ones are not. But... would it help to be able to mark some items (eg. the control sample) as "Not suitable for inheriting annotations"? It could be a boolean flag that causes the automatic function to ignore annotations on it. Comments? > We have to inherit from just one of the two biosources because BASE doesn't > know which is experimental (ch1) and which is control (ch2). BASE will later > choose one arbitrarily (in Experiment Explorer for example). No, this was a bug that was fixed in BASE 2.5. Since then, all inherited annotations are displayed and can be used in the analysis. /Nicklas ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
