Re: [Psidev-ms-dev] mzML 0.99.0 comments

[Matthew C. <mat...@va...>]

Oops.  It killed my spaces.  Let me try again.

That sounds like a pretty good way to distinguish between values 
(instances) and categories (classes) to me! Further, the instance_of 
relationship can be used in addition to the current part_of and is_a 
relationships and it will serve to disambiguate a branch of the CV where 
the actual category that a value belongs to is an ancestor instead of a 
direct parent. For instance:

MS:1000173 "MAT900XP"
--is a MS:1000493 "Finnigan MAT"
----part of MS:1000483 "Thermo Fisher Scientific"
------is a MS:1000031 "model by vendor"
--------part of MS:1000463 "instrument description"
----------part of MS:0000000 "MZ controlled vocabularies"

What category does the controlled value "MAT900XP" belong to, i.e. if we 
used cvParam method B, would it look like:
<cvParam cvLabel="MS" categoryName="Finnigan MAT" 
categoryAccession="MS:1000493" accession="MS:1000173" name="MAT900XP"/>
Or would it look like:
<cvParam cvLabel="MS" categoryName="model by vendor" 
categoryAccession="MS:1000031" accession="MS:1000173" name="MAT900XP"/>

Of course I think it should be the latter, but how would you derive that 
from the CV? You can't, unless you add a new relationship or convention, 
so I suggest:

MS:1000173 "MAT900XP"
--instance of MS:1000031 "model by vendor"
--is a MS:1000493 "Finnigan MAT"
----part of MS:1000483 "Thermo Fisher Scientific"
------is a MS:1000031 "model by vendor"
--------part of MS:1000463 "instrument description"
----------part of MS:0000000 "MZ controlled vocabularies"

It would also be good to get rid of the MS:1000483->MS:1000031 
relationship at that point because "Thermo Fisher Scientific" is NOT an 
instrument model.

-Matt

Matthew Chambers wrote:
> That sounds like a pretty good way to distinguish between values 
> (instances) and categories (classes) to me! Further, the instance_of 
> relationship can be used in addition to the current part_of and is_a 
> relationships and it will serve to disambiguate a branch of the CV 
> where the actual category that a value belongs to is an ancestor 
> instead of a direct parent. For instance:
> MS:1000173 "MAT900XP"
> is a MS:1000493 "Finnigan MAT"
> part of MS:1000483 "Thermo Fisher Scientific"
> is a MS:1000031 "model by vendor"
> part of MS:1000463 "instrument description"
> part of MS:0000000 "MZ controlled vocabularies"
> What category does the controlled value "MAT900XP" belong to, i.e. if we
> used cvParam method B, would it look like:
> <cvParam cvLabel="MS" categoryName="Finnigan MAT" 
> categoryAccession="MS:1000493" accession="MS:1000173" name="MAT900XP"/>
> Or would it look like:
> <cvParam cvLabel="MS" categoryName="model by vendor" 
> categoryAccession="MS:1000031" accession="MS:1000173" name="MAT900XP"/>