Issue 5487: order attribute be be added for BioDataCube in model (and, hence, the DTD) (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, an order attribute be added
for 
BioDataCube in the model (and, hence, the DTD).  This will specify the order
of 
the dimensions in the accompanying data specified by either the DataInternal
or
DataExternal element.  In addition, the rule specifying "the first dimension
matches 
order of BioAssayDimension, second, the DesignElementDimension and the
third, the 
QuantitationDimension" can be removed.
Attribute to add: BioDataCube.order
type: enum {BDQ | BQD | DBQ | DQB | QBD | QDB}
default: 'BDQ'


The following will be effected by this change:
The model and MAGE.xmi file.
The DTD
Section 3.1.12, "BioAssayData" of the submission


(MAGE Issue 25)

Resolution: see below
Revised Text: Changes to the specification:
Section 2.1.12, "BioAssayData":
Figure 2.13 will be updated 
The BioAssayCube documentation will add to its Associations section after the documentation of its cube attribute:
\border\b : Order (default: \iBDQ\i)
enumeration {\iBDQ\i | \iBQD\i | \iDBQ\i | \iDQB\i | \iQBD\i | \iQDB\i}
The order to expect the dimension. The enumeration uses the first letter of the three dimensions to represent the six possible orderings.
(where \b...\b indicates bold and \i...\i indicates italics) 
 
 Changes to Section 3.1.4.5. 
The ATTLIST declaration for BioDataCube is replaced.
Currently:
"<!ATTLIST BioDataCube %BioDataValues_attrs; >"
Becomes:
"<!ATTLIST BioDataCube %BioDataValues_attrs;
order (BDQ|BQD|
DBQ|
DQB|
QBD|
QDB) "BDQ" >" 
 
 The model and MAGE.xmi file is modified to add the order attribute to BioDataCube. 
 
 The MAGE-ML.dtd:
Modify the Element and Attlist declarations for BioDataCube
Currently:
" Attributes

Inherites attributes from base class BioDataValues."

Becomes:

" Attributes

Inherites attributes from base class BioDataValues.

order: The order to expect the dimension. The enumeration uses 

the first letter of the three dimensions to represent the six 

possible orderings."

Currently:
"<!ATTLIST BioDataCube %BioDataValues_attrs; >"
Becomes:
"<!ATTLIST BioDataCube %BioDataValues_attrs;
order (BDQ|
BQD|
DBQ|
DQB|
QBD|
QDB) "BDQ" >" 

Actions taken:
July 14, 2002: received issue
December 11, 2002: closed issue
Discussion: 
This will specify the order of the dimensions in the accompanying data specified by either the DataInternal or DataExternal element. In addition, the rule specifying "the first dimension matches order of BioAssayDimension, second, the DesignElementDimension and the third, the QuantitationDimension" can be removed
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, an order attribute be
added
for 
BioDataCube in the model (and, hence, the DTD).  This will specify the
order
of 
the dimensions in the accompanying data specified by either the
DataInternal
or
DataExternal element.  In addition, the rule specifying "the first
dimension
matches 
order of BioAssayDimension, second, the DesignElementDimension and the
third, the 
QuantitationDimension" can be removed.
Attribute to add: BioDataCube.order
type: enum {BDQ | BQD | DBQ | DQB | QBD | QDB}
default: 'BDQ'


The following will be effected by this change:
The model and MAGE.xmi file.
The DTD
Section 3.1.12, "BioAssayData" of the submission


(MAGE Issue 25)