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

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Regarding, RDF I would like to suggest that this is not an option at
this time. RDF was in fact suggested at the DC meeting, and it was
concluded that it is such a departure from current formats, that we
cannot support it at this time. We do not have the resources to pull it
off.

=20

Having said that, I would summarize RDF as the antithesis of everything
you want out of mzML. RDF can be oversimplified (by me) as essentially a
listing of facts of:

  Subject verb predicate

wherein each noun and verb is carefully defined in an ontology (not just
a controlled vocabulary) such that true meaning can be inferred from
unstructured data.  So, in pseuoRDF, our documents would go like this:

=20

Eric has_produced this_mzML_document

Eric is_a contact

Eric has_full_name Eric Deutsch

Eric has_email_address ede...@fu...o

This_mzML_document is_a mzML_document

This_mzML_document contains_a_run run1

Spectrum1 was_generated_in_run run1

Spectrum1 has_type precursor_ion_scan

=20

The structure is that there is no structure. You are free to list every
fact that is relevant in any order. However, each noun and verb must be
defined in the context of an ontology (or probably multiple ontologies).

=20

The beauty is that no one ever needs to argue about xsd schemas or two
different formats for the same thing any more. Wheee!

=20

The um, downside, is that your software to deal (effectively) with it
needs to be 10x more brilliant than the best piece of code you've
written so far.

=20

Cheers,

Eric

=20

=20

=20

________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of Brian
Pratt
Sent: Monday, October 08, 2007 4:14 PM
To: psi...@li...
Subject: Re: [Psidev-ms-dev] more is_a vs. part_of errors?

=20

Hi Angel,

=20

This may be a bit esoteric, but I wanted to ask what advantage RDF might
have over the older W3C XML schema (.xsd).  I'm unfamiliar with RDF, and
from my 20 minutes of googling it appears rather more complex than .xsd
- certainly more complex than it would need to be to handle the kinds of
things mzData and mzXML do today, but I'm sure I'm flaunting my
ignorance. =20

=20

I see that there are (but don't completely understand the nature of)
relationships between RDF, OWL, OBO, and CV.  Presumably you see some
means of exploiting these relationships?  I have a lot to learn if we go
this route, but it sounds interesting.  At least we'd get to say
"semantic web" a lot, which sounds cool.

=20

>> I believe that there is an OBO to RDF perl tools someplace.

Maybe this (java, I think):

http://www.cs.utexas.edu/~hamid/research/obo2owl.cgi

=20

=20

Thanks,

=20

Brian

=20

________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of Angel
Pizarro
Sent: Saturday, October 06, 2007 5:17 PM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] more is_a vs. part_of errors?

=20

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.=20

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.=20

- 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=20
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:=20
>
> 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"=20
>
> 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"=20
>
> 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"=20
>
> 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"=20
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000106 "on"
>
> is a MS:1000021 "reflectron state"
>
> part of MS:1000480 "analyzer attribute"=20
>
> 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"=20
>
> 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=20
> all the other vendors:
>
> MS:1000495 "Applied Biosystems"
>
> part of (IS_A) MS:1000121 "ABI / SCIEX"
>
> is a MS:1000031 "model by vendor"
>=20
> 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"=20
>
> 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"=20
>
> 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"=20
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000174 "MAT900XP Trap"
>
> is a MS:1000493 "Finnigan MAT"=20
>
> 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"=20
>
> is a MS:1000031 "model by vendor"
>
> part of MS:1000463 "instrument description"
>
> part of MS:0000000 "MZ controlled vocabularies"
>
> MS:1000172 "MAT253"=20
>
> 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"=20
>
> 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
>=20

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--=20
Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

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