[Psidev-ms-dev] CV is broken?

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

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/control
ledVocabulary/psi-ms.obo>
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