[Mged-mage] 'reference' in MAGE ??

[White, J. A. <JW...@ti...>]

Hello,

In recent discussions in the Ontology Working Group the subject of reference
samples was discussed.  Many microarray experiments are designed with common
references for comparison.  These are often pools of RNA from several cell
lines, pools of RNA from several tissues, etc.  

These can be described by creating a BioSource for each cell line in the
pool and BioSample that represents the entire pool.  This is not very
convenient at all, especially when that pool of RNA is provided
commercially.  They also can be created as a BioSource with a full
Description of the RNAs included.  

Normally, the reference sample is not an ExperimentalFactor, i.e. we don't
normally compare expression between reference samples.  However, this is a
possible, e.g. in cases where one compares data from different sets of
experiments using different reference samples, or when the reference sample
for a study is changed for whatever reason.  In these cases the reference
sample would be an ExperimentalFactor.  

So, I have 2 questions for you all:

1) Does the MAGE-OM have any concept or object that could be used to
indicate that a sample is a reference for comparison?
2) Has anyone had a need to compare reference samples for any reason?  

The issue is whether or not to define terms for these reference samples.  

Thanks for any information you can provide us.  

Joe White
TIGR