Issue 5488: dimension elements be transformed to be optional (gene-expression-ftf)
Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody)
Nature: Uncategorized Issue
Severity: 
Summary: Recommend that, in additional to MAGE Issue 11, the dimension elements be
transformed
to be optional, since the transformation of BioDataTuples makes specifying
the 
dimensions redundant.


The following will be effected by this change:
The DTD
(by modifying the generating code:
generate_dtd\TransformBioAssayData.java,
generate_classes\CreateFile.java)
Section 4.1.4, "Transforming BioDataValues" of the submission

Resolution: see below
Revised Text: Changes to Section 3.1.4.4 of the specification:
An additional rule is added between the current rules 1 and 2:
"2: The dimension associations of BioAssayData are transformed to have cardinalities 0..1 from 1..1" 

 The DTD
(by modifying the generating code:
generate_dtd\TransformBioAssayData.java,
generate_classes\CreateFile.java)
Currently:
"<!ENTITY % BioAssayData_content "(%Identifiable_content;),
SummaryStatistics_assnlist?,
BioAssayDimension_assnref,
DesignElementDimension_assnref,
QuantitationTypeDimension_assnref,
BioDataValues_assn?" >"
Becomes:
"<!ENTITY % BioAssayData_content "(%Identifiable_content;),
SummaryStatistics_assnlist?,
BioAssayDimension_assnref?,
DesignElementDimension_assnref?,
QuantitationTypeDimension_assnref?,
BioDataValues_assn?" >" 

Actions taken:
July 23, 2002: received issue
December 11, 2002: closed issue
Discussion: 
In additional to Issue #5486, the dimension elements be transformed to be optional, since the transformation of BioDataTuples makes specifying the dimensions redundant.

End of Annotations:=====
X-Server-Uuid: F7D3E4A3-3C15-41D2-AC5D-A7D3F094E28F 
From: "Miller, Michael (Rosetta)" <Michael_Miller@Rosettabio.com> 
To: "'Juergen Boldt'" <juergen@omg.org> 
cc: "'GE FTF'" <gene-expression-ftf@omg.org> 
Subject: Issues for GE Specification 
Date: Sun, 14 Jul 2002 15:46:45 -0700 
X-Mailer: Internet Mail Service (5.5.2653.19) 
X-WSS-ID: 112F21B171906-01-01 


Hi Juergen,


Here's the first batch of issues for the Gene Expression FTF
(dtc/02-02-05).
Also, since the DTD and the XMI files are normative, shouldn't they be
available from the FTF site, along with the specification?  The DTD in
particular is important.  We've assigned private issue numbers (which
aren't
particularly consecutive) to some of the issues which I'm noting--I'm
expecting them to get an entirely different issue number from you that
the
FTF will refer to!


For others who might want to raise issues, should they send directly
to you
or is there an appropriate e-mail address?


thanks,
Michael


Michael Miller
Senior Application Developer
Rosetta Biosoftware
michael_miller@rosettabio.com
www.rosettabio.com


Recommend that, in additional to MAGE Issue 11, the dimension elements
be
transformed
to be optional, since the transformation of BioDataTuples makes
specifying
the 
dimensions redundant.


The following will be effected by this change:
The DTD
(by modifying the generating code:
generate_dtd\TransformBioAssayData.java,
generate_classes\CreateFile.java)
Section 4.1.4, "Transforming BioDataValues" of the submission