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

[Angel P. <an...@ma...>]

I wouldn't spend too much time trying to parse OBO files into XML schema.
The format grew out of a need for quick and dirty CV with some ontology
structure editing and there is really only one library editor that works
with it, namely the author's tools of the OBO format itself.

As a side note, and completely my own opinion, but if mzML were to use RDF
schema for the schema and RDF for the CV, validation and everything else
would fall into place. I believe that there is an OBO to RDF perl tools
someplace.

- angel

On 10/6/07, Matt Chambers <mat...@va...> wrote:
>
> 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
> >
>
>
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-- 
Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
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