RE: [Mged-mage] Valid MAGE-ML export

[Kjell P. <kj...@ii...>]

Hi Michael,

On Wed, 23 Jul 2003, Miller, Michael (Rosetta) wrote:

> Hi Kjell,
> 
> > Would a MAGE-ML document containing BioAssayData objects, but not 
> > including all the corresponding BioDataValues objects, be valid ?
> 
> Yes, but I say that because 'valid' is an XML term that means nothing more
> than that the XML document conforms to the DTD.  So, of more interest is
> whether that it is useful.
> 
> I think one use case that would be of interest is a researcher looking at
> the different ways people did their gene expression experiments--he/she is
> not at all interested in the data at the moment, he/she is interested in the
> algorithms used to normalize and remove error, how replicates were done and
> how many.  All this information is with the BioAssayData and its related
> objects, Transformation and the Mappings, and doesn't require downloading
> the BioDataValues.  

This is pretty much our situation. We want to document a pipeline of 
analysis including transformations and clustering, describe each step
in detail, not include all intermediate BioDataValues, but only for the 
input data and the resulting data.

> > The filled diamond containment symbol (of the +bioDataValues 
> > association) 
> > implies "no", but the textual description of BioAssayData in 
> > the spec. 
> 
> Actually, the relevant fact is the cardinality of 0..1 on the bioDataValues
> end of the association, that makes it optional.  The filled in diamond says
> that if there is a BioDataValue, it's lifetime is controlled by the
> BioAssayData.

Thanks for clearifying this! I focused on the wrong side of the 
association, reading cardinality 1 beside the diamond as compulsory 
instead...


Thanks,
Kjell 


> > -----Original Message-----
> > From: Kjell Petersen [mailto:kj...@ii...] 
> > Sent: Wednesday, July 23, 2003 6:01 AM
> > To: Mged Mage list at SourceForge
> > Subject: [Mged-mage] Valid MAGE-ML export
> > 
> > 
> > 
> > Hi all,
> > 
> > A quick question about export of valid MAGE-ML / use of the MAGE-OM :
> > 
> > Would a MAGE-ML document containing BioAssayData objects, but not 
> > including all the corresponding BioDataValues objects, be valid ?
> > 
> > The filled diamond containment symbol (of the +bioDataValues 
> > association) 
> > implies "no", but the textual description of BioAssayData in 
> > the spec. 
> > says : 
> > 
> > "BioAssayData is the entry point to the values. Because the 
> > actual values 
> > are represented by a different object, BioDataValues, which 
> > can be memory 
> > intensive, the  annotation of the transformation can be 
> > gotten seperate 
> > from the data."
> > 
> > hints at the opposite as a design goal ?
> > 
> > Is BioDataValues in practice seperable from BioAssayData when 
> > working with 
> > the MAGE-OM ?
> > 
> > 
> > Cheers,
> > Kjell
> > 
> > 
> > -- 
> > Kjell Petersen
> > Researcher
> > 
> > Computational Biology Unit                  Bioinformatics group
> > Bergen Center for Computational Science     Department of Informatics
> > Unifob A/S                                  University of Bergen
> > 
> > 
> > 
> > 
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> 

-- 
Kjell Petersen
Researcher

Computational Biology Unit                  Bioinformatics group
Bergen Center for Computational Science     Department of Informatics
Unifob A/S                                  University of Bergen