Re: [Gusdev-rad-issues] Linking Treatment with ElementResultImp

[Elisabetta M. <man...@pc...>]

Hi Sucheta, here is the way it works:

1. Entries in ElementResultImp point to Quantifications (which in turn 
point to the image analysis protocols); Quantifications point to 
Acquisitions (which in turn point to scanning protocols); Acquisitions 
point to Assays (which in turn point to the Arrays and to hybridization 
protocols).

2. An Assay corresponds to a one or two channel hybridization, so it will 
involve the RNA samples (or more precisely the labeled extracts obtained 
from these samples) that are hybridized to it.

3. Information about samples is stored in the various Biomaterial tables 
which include the Treatment tables. One can store the whole process from 
the original BioSource (e.g. "mouse", "mouse liver", "cell culture dish") 
to derived BioSamples (e.g. aliquots, RNAs, intermediate treatments etc.) 
to derived (from the BioSamples) LabeledExtracts. Each such derivation 
corresponds to a treatment stored in the Treatment table. Treatment 
points to the *output* of the treatment. BioMaterialMeasurement points to 
Treatment and to the *input* of that Treatment). This is pretty much 
straight from the MAGE model.
For concrete examples of these, you might look at the 3 Examples at 
https://www.cbil.upenn.edu/RAD/tutorial/ModuleIII.html.

4. Each Assay is linked to all BioMaterials (BioSources, BioSamples, 
LabeledExtracts) corresponding to it via the AssayBioMaterial table. There 
is also a redundant table (which can be useful to expedite queries) which 
links each Assay to the LabeledExtracts corresponding to it (i.e. the last 
step in the chain from BioSources to LabeledExtracts).

Thus to go from ElementResultImp to Treatments attached to the assay at 
hand, one goes up to Assay through Quantifications->Acquisitions->Assay, 
then can get all BioMaterials relative to that Assay through 
AssayBioMaterial, then get the Treatments pointing to those BioMaterials.

Hope this helps.
Elisabetta

---

On Sun, 2 Oct 2005, Sucheta Tripathy wrote:

> Hello Group,
>
> Another question. Since we have a large number of experiments and as I 
> understand we describe the treatment to each biological material in 
> RAD::Treatment table(Hope that is the way). However, I don't know how can I 
> link the raw .cel data for each experiment, that goes to ElementResultImp to 
> the Treatment table.
>
> Many thanks
>
> Sucheta 
>
>
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