Issue 5559: Attribute to be added to describe its type (gene-expression-ftf)
Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody)
Nature: Uncategorized Issue
Severity: 
Summary: Request from Hilmar Lapp, GNF, and Michael Miller, Rosetta Biosoftware,
that an attribute be added to Parameter to describe its type:
  - name: type
  - required: true
  - enumeration: {IN, INOUT, OUT}
  - default: IN
  
This would allow Protocol/ProtocolApplication to allow return values.


Resolution: No Action Taken.
Revised Text: 
Actions taken:
July 29, 2002: received issue
December 11, 2002: closed issue
Discussion: 
Request from Hilmar Lapp, GNF, and Michael Miller, Rosetta Biosoftware, that an attribute be added to Parameter to describe its type:

- name: type

- required: true

- enumeration: {IN, INOUT, OUT}

- default: IN

This would allow Protocol/ProtocolApplication to allow return values

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




Request from Hilmar Lapp, GNF, and Michael Miller, Rosetta
Biosoftware,
that an attribute be added to Parameter to describe its type:
  - name: type
  - required: true
  - enumeration: {IN, INOUT, OUT}
  - default: IN
  
This would allow Protocol/ProtocolApplication to allow return values.


(MAGE ISSUE 112) 


User-Agent: Microsoft-Entourage/9.0.1.3108 
Date: Fri, 23 Aug 2002 17:38:25 -0700 
Subject: Re: Final Issues: Preview for comments 
From: Karl Konnerth <konnerth@incyte.com> 
To: <gene-expression-ftf@omg.org> 


on 8/21/02 4:08 PM, Miller, Michael (Rosetta) at
Michael_Miller@Rosettabio.com wrote:


> 2) In call_to_vote_08_31_02.txt, where I suggest alternatives, if I
     don't
> receive any feedback, I plan to go with the first alternative.  If I
     receive
> feedback but it falls equally on both sides, I'll submit both to the
     FTF and
> let that vote be final.


Hi,


I don't have strong opinions on these but here are my recommendations
on a
few of them:


> Issue #5550: Allowing a person to belong to only one organization is
> too restrictive.
> ====================================================================
> 
> Request to allow a person to belong to more than one organization.
> 
> Alternative One:
> Recommend take no action.
> 
> Not clear if any benefit in the scope of the specification is gained
> by this.  Version two may reconsider this.


I agree.  I would think that in context of gene expression, a person
could
identify a single organization that is relevant.  I don't see why
multiple
organizations are that important.


> Issue #5559: Attribute to be added to describe its type
> =======================================================
> 
> Parameters for Protocols can not only be input parameters but can be
> output parameters or both input and output parameters.  This would
> allow
> Protocol/ProtocolApplication to allow return values.  An example of
> an
> output parameter from FeatureExtraction could be "Mean Average
> Backround
> Subtraction"
> 
> Alternative One:
> Recommend no action.
> 
> Could be considered for version two.
> 
> Alternative Two:
> Recommend an attribute be added to Parameter to describe its type:
>  - name: type
>  - required: true
>  - enumeration: {IN, INOUT, OUT}
>  - default: IN


I favor no action.  This makes the protocol parameter attributes more
complex, and also appears to complicate the interfaces.


> Issue #5561: Group BioSequences that share the same type,
  PolymerType,
> and Species information
>
  ======================================================================
> 
> It would be useful to have a way to group BioSequences that share
  the same
> Type, PolymerType, and Species information.  This would allow the
  XML
> files with BioSequences to be a great deal smaller.
> 
> Recommend no action.
> 
> Could be considered for version two.  Any change would probably
  greatly effect
> existing implementations.
> 
> (Steve Cherwitz may have a suggested alternative that could make
  version one)


I favor no action (unless Steve has a good solution).  Yes, this might
make
the files smaller, but at a cost of making the XML files themselves
and file
processing algorithms more complicated.  Do we have any idea as to how
often
this grouping would be used in practice?


Best regards,


---Karl


P.S. Do you get the feeling that I favor simplicity?  Yes, especially
when
it comes to standards.  A challenge is to resist adding more and more
features until the standard collapses under its own weight.  On the
other
hand, if a new feature would make it usable for someone who otherwise
could
not use the standard, I would consider it.