Bob MacCallum wrote: > > Nicklas Nordborg writes: > > I really don't see how a 'channel' attribute could help answer that > > question. Everything upstreams of the raw bioassay is generally speaking > > not accessible in the analysis module. The only upstreams information > > you can use are annotations that have been inherited to the raw > > bioassays and specified as experimental factors of the experiment. For a > > single raw bioassay this should be either 'male' or 'female'. The > > So even though the two samples/biosources each have an annotation (one "male" > one "female"), you would recommend that the raw bioassay should inherit only > from one.
By default inheriting multiple annotations of the same type is reported as an error by the experiment validator tool. This can of course be changed to warning or ignore, but I suspect that downstream analysis tools and plug-ins can get confused. The tools/plug-ins we have created are works on the bioassay level as the smallest entity, ie. if you create group things together the entire bioassay must belong to the same group. It seems like your case wants ch1 to belong to the "male" group and ch2 to belong to the "female" group (or the other way around). > As discussed here: > http://www.mail-archive.com/[EMAIL PROTECTED]/msg00907.html > inheriting from more than one item leads to undefined behaviour. This is a bug that has been fixed in the 2.5 release. > I'd like to suggest that one should be able to inherit annotations from > multiple biosources in a defined order (e.g. ch1, ch2). > > Alternatively, some innate ordering of the labelled extracts with respect to > hyb (again in channel order). None of the above seems possible with the current database design and backwards compatibility issues. It would be a thing for BASE 3. Even if that information did exist in the database, there is no guarantee that the data was imported in that way. That would require the importer to be more intelligent than just copying values from a text file column into the database. It would have to match the "dye" for the column to a labeled extract's dye and then verify this against what has been defined in the raw-data-types.xml file. But, everything can still be re-linked to other items after the import so it could still not be "trusted". /Nicklas ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
