psidev-ms-dev

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

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

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

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
>

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
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

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

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

Hi Angel,

 

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.  

 

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.

 

>> 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

 

 

Thanks,

 

Brian

 

  _____  

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?

 

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
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736 
F: 215-573-9004 

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

[Mike C. <tu...@gm...>]

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'm not sure I understand the implications of this.  If the CV gets
rearranged after the spec is out and people are using mzML file, will
this be a problem?  Does it matter if the CV usage in the mzML in
front of me does not match my CV database?  Or do I need to have all
versions of the CV database?

Mike

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

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

The backward compatibility problem is not unique to CVs; backwards 
compatibility is just as much a problem with XML schema.  If there is 
ever a change to the schema or CV which moves or deletes an existing 
term, old files are likely to be invalidated. This can be avoided by 
never moving or deleting existing terms, or if the appearance of moving 
and deleting terms can't be avoided, then adding support for deprecating 
instead of deleting.

-Matt

Mike Coleman wrote:
> 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'm not sure I understand the implications of this.  If the CV gets
> rearranged after the spec is out and people are using mzML file, will
> this be a problem?  Does it matter if the CV usage in the mzML in
> front of me does not match my CV database?  Or do I need to have all
> versions of the CV database?
>
> Mike
>
>   

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

[Chris T. <chr...@eb...>]

Hiya.

I think deprecation is pretty standard and is implemented for 
PSI CVs iirc. That way a term is not substantively changed, just 
flagged as deprecated with a pointer to the new preferred term 
and therefore nothing breaks (although terms are obviously added 
elsewhere as part of the process, but then they will be being 
added all the time anyway so a frozen CV is not that great an 
idea but updates need not be nightly as say OLS is (again, iirc)).

Cheers, Chris.


Matt Chambers wrote:
> The backward compatibility problem is not unique to CVs; backwards 
> compatibility is just as much a problem with XML schema.  If there is 
> ever a change to the schema or CV which moves or deletes an existing 
> term, old files are likely to be invalidated. This can be avoided by 
> never moving or deleting existing terms, or if the appearance of moving 
> and deleting terms can't be avoided, then adding support for deprecating 
> instead of deleting.
> 
> -Matt
> 
> Mike Coleman wrote:
>> 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'm not sure I understand the implications of this.  If the CV gets
>> rearranged after the spec is out and people are using mzML file, will
>> this be a problem?  Does it matter if the CV usage in the mzML in
>> front of me does not match my CV database?  Or do I need to have all
>> versions of the CV database?
>>
>> Mike
>>
>>   
> 
> 
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> Still grepping through log files to find problems?  Stop.
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> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://mibbi.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

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

[Eric D. <ede...@sy...>]

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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Still grepping through log files to find problems?  Stop.
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_______________________________________________
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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

P: 215-573-3736=20
F: 215-573-9004=20

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

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

All good points by Eric, RDF can indeed be simplified to just the triplet
tuple he mentions. The part he  glosses over though is RDF schema, an this
is where the main structure of an ontology is defined and constraints are
defined  on what (and maybe when / where, but don't quote me) you can put
terms and values in instance RDF documents. Notice I used "ontology", not
standard or data format. While we can bastardize an mzML written as RDFS an=
d
name a version as a standard, this is not really done in the RDF world.
RDFS are released on fairly short timelines as new terms or changes are
approved by a committee, so  RDFS/RDF is more likely to be of use to the CV
development team, certainly not the schema development efforts.

An overriding concern of mine, though, is time. The mzML schema
specification should in no way be held up by any issues dealing with RDFS
and RDF, even the CV. Everyone is to invested in getting the product out th=
e
door. Standards don't need to be perfect, they just have to work (credit to
Norman)

So I am sorry to have brought it up, but hopefully Eric has shut the door o=
n
that option for mzML v1

-angel

On 10/8/07, Eric Deutsch <ede...@sy...> wrote:
>
>  Regarding, RDF I would like to suggest that this is not an option at thi=
s
> time. RDF was in fact suggested at the DC meeting, and it was concluded t=
hat
> 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.
>
>
>
> 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:
>
>
>
> 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
>
>
>
> 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).
>
>
>
> The beauty is that no one ever needs to argue about xsd schemas or two
> different formats for the same thing any more. Wheee!
>
>
>
> 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.
>
>
>
> Cheers,
>
> Eric
>
>
>
>
>
>
>   ------------------------------
>
> *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?
>
>
>
> Hi Angel,
>
>
>
> 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 =
=96
> 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=
.
>
>
>
> I see that there are (but don't completely understand the nature of)
> relationships between RDF, OWL, OBO, and CV.  Presumably you see some mea=
ns
> 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.
>
>
>
> >> 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<http://www.cs.utexas=
.edu/%7Ehamid/research/obo2owl.cgi>
>
>
>
>
>
> Thanks,
>
>
>
> Brian
>
>
>  ------------------------------
>
> *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?
>
>
>
> 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 RD=
F
> 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
> >
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
>
>
> --
> 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
>
> P: 215-573-3736
> F: 215-573-9004
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>


--=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

P: 215-573-3736
F: 215-573-9004