Re: [Psidev-ms-dev] CV is broken?

[Brian P. <bri...@in...>]

That's how it looks to me too.  I think this needs to be fixed, as I
understand it the ontology is meant to be free of ambiguous terms.

Thanks,

Brian

-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of Chris
Taylor
Sent: Friday, October 05, 2007 5:11 PM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] CV is broken?

Actually I think the problem here is overloading of a term -- 
the thing is used in two different ways -- there is a 
description of the physical reality of the ion source (it does 
DE) and there is a term in a description -- really the problem 
here is that what is implied is that either a datum is part of 
the ion optics of the physical instance of a mass spec, or that 
a description (an abstract that can be manifest in files or 
whatever) contains a physical entity (DE-source bits). I think 
that's it anyway. So really the issue is the combination of two 
related but different things in one concept. Am I right?

Brian Pratt wrote:
> I think we have some early fruit from my messing around with OBO->W3C 
> schema conversion.
> 
>  
> 
> In the CV file 
>
http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controll
edVocabulary/psi-ms.obo 
> there is exactly one term that claims both an is_a and part_of
relationship:
> 
>  
> 
> [Term]
> 
> id: MS:1000246
> 
> name: delayed extraction
> 
> def: "The application of the accelerating voltage pulse after a time 
> delay in desorption ionization from a surface. The extraction delay can 
> produce energy focusing in a time-of-flight mass spectrometer." [PSI:MS]
> 
> exact_synonym: "DE" []
> 
> is_a: MS:1000462 ! ion optics
> 
> relationship: part_of MS:1000456 ! precursor activation description
> 
>  
> 
> Let's follow the inheritance chains:
> 
>  
> 
> MS:1000246 "delayed extraction"  is_a
> 
> MS:1000462 "ion optics" part_of
> 
> MS:1000463 "instrument description"  part_of
> 
> MS:0000000 "MZ controlled vocabularies"
> 
>  
> 
> And also,
> 
>  
> 
> MS:1000246 "delayed extraction" part_of
> 
> MS:1000456 "precursor activation description" part_of
> 
> MS:1000442 "spectrum" part_of
> 
> MS:0000000 "MZ controlled vocabularies"
> 
>  
> 
> So:
> 
> A is a kind of B
> 
> A is a part of C
> 
> B is not a part of C
> 
>  
> 
> This would appear to violate the transitive property of the is_a and 
> part_of relationships.  Normally in discussing inheritance one views "is 
> a" and "has a" (or in the topsy-turvy world of OBO, "part of") as being 
> distinct and mutually exclusive ideas.
> 
>  
> 
> Actually the format itself is a bit of a surprise, I had anticipated 
> "is_a" being an enumerated type of "relationship" as "part_of" is.  If 
> this MS:1000246  is simply a victim of a clerical error, as I suspect it 
> is, then a tidier representation of inheritance would have helped catch 
> the problem sooner.
> 
>  
> 
> - Brian
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

-- 
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://mibbi.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

-------------------------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems?  Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev