Issue 5551: QuantitationType issue (gene-expression-ftf)
Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody)
Nature: Uncategorized Issue
Severity: 
Summary: Allowing a QuantitationType to know how it was derived 
would make navigation easier.


Request from Ugis Sarkans, EBI, that the Target association be 
navigable from QuantitationType to QuantitationTypeMap.  The 
association end would be named quantitationTypeMaps.


(MAGE ISSUE 108)

Resolution: see below
Revised Text: Changes to the Specification:

Section 2.1.12, BioAssayData

Replace Figure 2-14

Section 2.1.17, QuantitationType

Add to the QuantitationType Association documentation:

Currently:

" \bconfidenceIndicators\b : ConfidenceIndicator (0..3)

The association between a 

ConfidenceIndicator and the 

QuantitationType its is an indicator for."

Becomes:

" \bconfidenceIndicators\b : ConfidenceIndicator (0..3)

The association between a 

ConfidenceIndicator and the 

QuantitationType its is an indicator for.

\bquantitationTypeMaps\b : QuantitationTypeMap (0..n)

The QuantitationType whose value will be 

produced from the values of the source 

QuantitationType according to the 

Protocol."

(where \b...\b represents boldface)

Replace Figure 2-20
 
 
  MAGE-OM and the generated MAGE.xmi are updated, changing the Target association between QuantitationType and QuantitationTypeMap.
 
 
  Modify Entities for QuantitationType

Currently:

" confidenceIndicators: The association between a 

ConfidenceIndicator and the QuantitationType its is an indicator 

for."

Becomes:

" confidenceIndicators: The association between a 

ConfidenceIndicator and the QuantitationType its is an indicator 

for.

quantitationTypeMaps: The QuantitationType whose value will be 

produced from the values of the source QuantitationType according to 

the Protocol."

Currently:

"<!ENTITY % QuantitationType_content "(%Identifiable_content;),

Channel_assnref?,

Scale_assn,

DataType_assn,

ConfidenceIndicators_assnreflist?" >"

Becomes:

"<!ENTITY % QuantitationType_content "(%Identifiable_content;),

Channel_assnref?,

Scale_assn,

DataType_assn,

ConfidenceIndicators_assnreflist?,

QuantitationTypeMaps_assnreflist?" >"

Modify Element and Attlist declarations for QuantitationType

Currently:

" confidenceIndicators: The association between a 

ConfidenceIndicator and the QuantitationType its is an indicator 

for."

Becomes:

" confidenceIndicators: The association between a 

ConfidenceIndicator and the QuantitationType its is an indicator 

for.

quantitationTypeMaps: The QuantitationType whose value will be 

produced from the values of the source QuantitationType according to 

the Protocol."
 

Actions taken:
July 29, 2002: received issue
December 11, 2002: closed issue
Discussion: 
Request from Ugis Sarkans, EBI, that the Target association be navigable from QuantitationType to QuantitationTypeMap. The association end would be named quantitationTypeMaps.

This also provides a workaround for Issue #5552, in that a Ratio, for instance, can reference a QuantitationTypeMap whose protocol describes how it was derived and the Map also references the QuantitationTypes used to derive the Ratio.

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: gene-expression-ftf@omg.org 
Subject: Gene Expression FTF issues 
Date: Mon, 29 Jul 2002 07:30:43 -0700 
X-Mailer: Internet Mail Service (5.5.2653.19) 
X-WSS-ID: 115B8FEF18115-01-01 


Hi Juergen,


Here's the last batch.  Officially, I guess I'm entering them but
these are
collated from the MGED efforts for which there is no clear consensus
yet.


thanks, as always,
Michael


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




Allowing a QuantitationType to know how it was derived 
would make navigation easier.


Request from Ugis Sarkans, EBI, that the Target association be 
navigable from QuantitationType to QuantitationTypeMap.  The 
association end would be named quantitationTypeMaps.


(MAGE ISSUE 108)