[MOBY-l] Someone please forward...

[Mark Wilkinson]

Hi all, 

could someone please forward this response to Michael?  I've tried
repeatedly to get it to him, but my institute's server is still being
blacklisted by some spam-filters :-(

thanks!

M
-----Forwarded Message-----
> From: Mark Wilkinson <markw at illuminae.com>
> To: Michael Jensen <mdjgf8 at mizzou.edu>
> Subject: [Fwd: [MISC] Returned mail: see transcript for details]
> Date: Tue, 23 Mar 2004 13:53:53 -0800
> 
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> > To: markw at illuminae.com
> > Subject: [MISC] Returned mail: see transcript for details
> > Date: Sat, 20 Mar 2004 14:12:17 -0600
> > 
> > The original message was received at Sat, 20 Mar 2004 14:10:15 -0600
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> > 451 biomoby.org: Name server timeout
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> > 
> > ______________________________________________________________________
> > From: Mark Wilkinson <markw at illuminae.com>
> > To: Michael Jensen <mdjgf8 at mizzou.edu>
> > Cc: mobyl <moby-l at biomoby.org>
> > Subject: Re: [MOBY] [MOBY-l] Suggestions for objects in new service...
> > Date: Sat, 20 Mar 2004 12:10:15 -0800
> > 
> > Hi Michael!  I'm excited to see you setting up services!
> > 
> > > So with this I need to have the input as some object. I found a  
> > > namespace called Global that this may fit in, but I am unsure. There is  
> > > an object named text-plain also, but I don't know if that works or not  
> > > either.
> > 
> > okay, first be sure that you aren't confusing namespaces with objects -
> > the two are different things.
> > 
> > I think for a service like this (which is very cool, by the way!) I
> > would register it as follows:
> > 
> > input:  plain-text, **no** namespace (i.e. all namespaces)
> > output:  ___???__, **no** namespace
> > 
> > now... for output object format we have a couple of choices.  The one
> > you suggest is fine, though I think we could put a bit more "semantics"
> > into it...  My instinct is to build the output in this way (also note
> > that in your example you have a Scored_string object that has TWO String
> > sub-components, and another Scored_string object that has only ONE
> > String sub-component... and that isn't allowed!):
> > 
> > Option 1: outputting a proprietary object 'keyword_score'
> > 
> > <Collection>
> > <Scored_string  namespace='$inputNS' id='$inputID'>
> > 	<String namespace='' id='' articleName='acronym'/>MAPK</String>
> > 	<Object namespace='Global_keyword' id='MAPK'
> > articleName="string_component"/>
> > 	<Long namespace='' id='' articleName="score">0.9088453834</Long>
> > </Scored_string >
> > <Scored_string  namespace='$inputNS' id='$inputID'>
> > 	<String namespace='' id='' articleName='acronym'/>
> > 	<Object namespace='Global_keyword' id='increase'
> > articleName='string_component'/>
> > 	<Long namespace='' id='' articleName='score'>0.06212399</Long>
> > </Scored_string >
> > </Collection>
> > 
> > or Option 2 - outputting a proprietary child of formatted-text:
> > 
> > <Simple>
> > <Scored_string_output_format namespace='$inputNS' id='$inputID'>
> > ACRONYM: MAPK
> > LONG FORM: mitogen-activated protein kinase
> > SCORE: 0.90884572798250385
> > 
> > NAME: MAPK
> > SCORE: 1
> > 
> > NAME: mitogen-activated protein kinase
> > SCORE: 1
> > 
> > NAME: increase
> > SCORE: 0.06212914418525689
> > 
> > NAME: We
> > SCORE: 1.0000000000000237e-300
> > </keyword_score_analysis_output>
> > 
> > 
> > There may be other options, but those are the most obvious to me.  The
> > choice really comes down to whether or not you have a well-recognized
> > flat-file format (i.e. one for which there exists a parser that could
> > also be a MOBY service)
> > 
> > > I am guessing there are other places where some kind of score is given  
> > > on analysis of something, so I don't think it is far off creating a new  
> > > object for this one. I don't know if global_keyword fits either, or  
> > > what to do with that namespace attribute.
> > 
> > Creating new objects is fine (encouraged!) since it increases the
> > semantics of your output - the ontology takes care of any problems
> > relating to interpretation/visualization of your output.
> > 
> > It's probably worth pointing out here that services are allowed to
> > output "secondary objects", and one might consider this as a place to
> > put the "score" component, **however** in this case that will not work,
> > because the score would be applied to the entire collection object,
> > rather than to the individual components as you require.  This is an
> > interesting insight for me, as it does expose a limitation in the
> > modelling system... 
> > 
> > > I am not well-versed in all of this, so any comments and suggestions  
> > > are very welcome! Thanks to Ken Steube for helping me get even this  
> > > far!!!
> > 
> > I second that - Ken is a real star!!! :-)
> > 
> > I hope that there this is helpful to you, 
> > 
> > Cheers!
> > 
> > M
-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre