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RE: magetab2magerdf

From: Michael Miller <mmiller@teranode.com>
Date: Wed, 6 Jan 2010 12:18:21 -0500
Message-ID: <6401DB16544A5B4AA279B921F43547EC066FCBC0@MI8NYCMAIL16.Mi8.com>
To: "Jim McCusker" <james.mccusker@yale.edu>
Cc: "Helena Deus" <helenadeus@gmail.com>, "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
hi jim,

 

i'm not an expert on XML RDF so take my comments with a grain of salt.

 

"Unless I have a bug, ..."

 

pretty sure you do, especially since there is no 'Array Data Matrix
File' column in the SDRF plus none of the raw data file names in the
ArrayExpress zip file appear to be referenced in the RDF (or at least
the one i checked) and the referenced raw file in the RDF doesn't exist
in Array Express for that experiment.

 

" I'm not sure that's the case."

 

you could be right, it could be just indentation being odd or that i'm
missing something.

 

cheers,

michael

 

 

From: Jim McCusker [mailto:james.mccusker@yale.edu] 
Sent: Wednesday, January 06, 2010 9:09 AM
To: Michael Miller
Cc: Helena Deus; w3c semweb HCLS
Subject: 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
Received on Wednesday, 6 January 2010 17:18:53 UTC

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