Re: [Psidev-ms-dev] more is_a vs. part_of errors?

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

Good catches in the CV. Who is in charge of maintaining it and are they 
reading this list? :) I agree with auto-generating a XML schema with 
full semantic relationships encoded in it, direct from the CV, but you 
haven't addressed the issue I mentioned earlier. To do the 
auto-generation into CV params (if we choose method A) will be very ugly 
but it will allow for synonyms on the category names and value names. To 
implement the cvParam categories as XML elements though, you lose the 
ability to have synonyms for category names (unless you use the 
accession number of the category as the element name, which makes me 
shudder), but the final schema would look a lot nicer.

-Matt

Brian Pratt wrote:
>
> There are a handful of other cases where it appears that the authors 
> have gotten “is a” and “part_of” confused. My proposed corrections (IN 
> CAPS) inline:
>
> MS:1000025 "magnetic field strength"
>
> part of MS:1000480 "analyzer attribute"
>
> is a (PART_OF) MS:1000451 "analyzer description"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000024 "final MS exponent"
>
> part of MS:1000480 "analyzer attribute"
>
> is a (PART_OF) MS:1000451 "analyzer description"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000022 "TOF Total Path Length"
>
> part of MS:1000480 "analyzer attribute"
>
> is a (PART_OF) MS:1000451 "analyzer description"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000014 "accuracy"
>
> part of MS:1000480 "analyzer attribute"
>
> is a (PART_OF) MS:1000451 "analyzer description"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000106 "on"
>
> is a MS:1000021 "reflectron state"
>
> part of MS:1000480 "analyzer attribute"
>
> is a (PART_OF) MS:1000451 "analyzer description"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000105 "off"
>
> is a MS:1000021 "reflectron state"
>
> part of MS:1000480 "analyzer attribute"
>
> is a (PART_OF) MS:1000451 "analyzer description"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> The following changes would make the Thermo and ABI stuff look like 
> all the other vendors:
>
> MS:1000495 "Applied Biosystems"
>
> part of (IS_A) MS:1000121 "ABI / SCIEX"
>
> is a MS:1000031 "model by vendor"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000176 "MAT95XP Trap"
>
> is a (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"
>
> MS:1000175 "MAT95XP"
>
> is a MS:1000493 "Finnigan MAT"
>
> part of (IS_A) 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"
>
> MS:1000174 "MAT900XP Trap"
>
> is a MS:1000493 "Finnigan MAT"
>
> part of (IS_A) 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"
>
> MS:1000173 "MAT900XP"
>
> is a MS:1000493 "Finnigan MAT"
>
> part of (IS_A) 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"
>
> MS:1000172 "MAT253"
>
> is a MS:1000493 "Finnigan MAT"
>
> part of (IS_A) 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"
>
> I still think there’s a schema in there, albeit jammed in slightly 
> sideways at the moment.
>
> - Brian
>