Issue 5928: association ExperimentDesign (gene-expression-ftf)
Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody)
Nature: Uncategorized Issue
Severity: 
Summary: The association ExperimentDesign should be 
Experiment(1..1)-->ExperimentDesign(1..n)


instead of


Experiment(1..1)-->ExperimentDesign(1..1)


and the association name and end role should become 'ExperimentDesigns' 
and 'experimentDesigns'


Discussion:
Raised by Angel Pizarro 9/9/02 and requested by the Ontology Group
Resolution: see below
Revised Text: Changes to the Specification:

Section 2.1.13, Experiment

Modify the documentation of the Experiment class:

Currently:

" \bexperimentDesign\b : ExperimentDesign (1..1)"

Becomes:

"\bexperimentDesigns\b : ExperimentDesign (1..n)"

Figure 2-15 is updated
 
 
 MAGE-OM and the generated MAGE.xmi are updated, modifying the current ExperimentDesign association.
 
 
 MAGE-ML.dtd

Modify Element declarations for Experiment

Currently:

"experimentDesign: The association to the description and…"

Becomes:

"experimentDesigns: The association to the description and…"

Currently:

"<!ELEMENT Experiment ((%Identifiable_content;),

                        Providers_assnreflist?,

                        AnalysisResults_assnreflist?,

                        BioAssayData_assnreflist?,

                        BioAssays_assnreflist?,

                        ExperimentDesign_assn) >"

Becomes:

"<!ELEMENT Experiment ((%Identifiable_content;),

                        Providers_assnreflist?,

                        AnalysisResults_assnreflist?,

                        BioAssayData_assnreflist?,

                        BioAssays_assnreflist?,

                        ExperimentDesigns_assnlist) >"

Currently:

"<!ELEMENT ExperimentDesign_assn (ExperimentDesign) >"

Becomes:

"<!ELEMENT ExperimentDesigns_assnlist (ExperimentDesign+) >"
 

Actions taken:
May 2, 2003: received issue
November 6, 2003: closed issue
Discussion: 
Raised by Angel Pizarro 9/9/02 and requested by the Ontology Group

Change to the association ExperimentDesign as follows:

Experiment(1..1)-->ExperimentDesign(1..n)

instead of

Experiment(1..1)-->ExperimentDesign(1..1)

and the association name and end role should become 'ExperimentDesigns' and 'experimentDesigns'

End of Annotations:=====
rver-Uuid: F7D3E4A3-3C15-41D2-AC5D-A7D3F094E28F 
From: "Miller, Michael (Rosetta)" <Michael_Miller@Rosettabio.com> 
To: "'mged mage'" <mged-mage@lists.sourceforge.net>, 
   "'gene-expression-ftf@omg.org'" <gene-expression-ftf@omg.org> 
Subject: RTF Issues 
Date: Thu, 1 May 2003 12:45:16 -0700 
X-Mailer: Internet Mail Service (5.5.2653.19) 
X-WSS-ID: 12AFA98819003-01-01 


All,


Finally getting this list of proposed changes out.  Many thanks to Ugis for
reminding me and helping to bring these out.


We are under a bit of a tight deadline due to the lateness of my putting
these together, the RTF report is due at the OMG on May 12th.  It is exactly
the same process as the FTF report was, so I would like to gather thoughts
and additional discussions on these issues and any other that people think
fall into the scope of MAGE v1.1.  Remember, v2.0 is where the major changes
will take place, these items are mainly changes to associations to make them
more usable and the doc/specifications changes made at the Stanford
Programming Jamboree.


I will be then mailing out a vote to the OMG Gene Expression Revised Task
Force whose members are:
Steve Chervitz, Affymetrix; Charles Troup, Agilent Technologies; Ugis
Sarkans, European Bioinformatics Institute; Michael Niemi, International
Business Machines; Tony Parsons,  Pfizer; Michael D Miller, Rosetta
Biosoftware Business Unit
Michael


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


These will change the DTD but looking at it from a developer point of view I
don't anticipate much problem being able to cope with either v1.0 or 1.1.


Currently I've specifying the doctype as:
<!DOCTYPE MAGE-ML SYSTEM "1.0/MAGE-ML.dtd">


and will use
<!DOCTYPE MAGE-ML SYSTEM "1.1/MAGE-ML.dtd">


for documents with the revised changes.  I've also been successful at going
to the OMG site go fetch the DTD at when receiving the SAX resolveEntity()
callback (though it is always good to have a backup location):
http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd


If any changes are accepted, there will then be posted a
http://schema.omg.org/lsr/gene_expression/1.1/MAGE-ML.dtd


List of Issues for the Gene Expression Revision Task Force (MAGE v1.1)
(The numbering is tentative, the OMG will assign their numbers when 
they are submitted)
Michael Miller
05/01/2003

RTF ISSUE 2:
The association ExperimentDesign should be 
Experiment(1..1)-->ExperimentDesign(1..n)


instead of


Experiment(1..1)-->ExperimentDesign(1..1)


and the association name and end role should become 'ExperimentDesigns' 
and 'experimentDesigns'


Discussion:
Raised by Angel Pizarro 9/9/02 and requested by the Ontology Group