Re: magetab2magerdf

On Wed, Jan 6, 2010 at 11:55 AM, Michael Miller <mmiller@teranode.com>wrote:

>  but the problem seems to be that ArrayDataMatrix is referencing the
> 'Derived Array Data Matrix File' column (which is different than a 'Array
> Data Matrix File' column) when it should be referencing the 'Array Data
> File' column, there is a nested DerivedArrayDataMatrix element which does
> look correct.  above looks like  E-MEXP-986-raw-data-1321832734 should be
> an ArrayDataFile element with a value of '2d1S15.txt.txt', not sure how the
> name of the file was gotten, there is no mention in the SDRF of a file of
> that name but it is similar in name to the file in the Derived Array Data
> Matrix file.   There is no mention of '2d1S15.txt.txt', the correct name,
> anywhere in the file.
>

Unless I have a bug, I'm following the DAG set out in the Limpopo data
structure. I can take a closer look at this tonight.

>  plus there also seems to be unnecessary duplication, i.e. there's a
> nested repeat of ArrayDataMatrix and DerivedArrayDataMatrix elements?   but
> this might be an artifice of XML RDF?
>
I'm not sure that's the case. See below.

>  does XML RDF allow referencing an element that is fully defined
> elsewhere?  that would make things a lot clearer and concise.
>
We are already doing that. Take a look at the ProtocolApplication elements,
which do exactly that.

Thanks,
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu