Re: [Psidev-ms-dev] Updated Ontology File

[Kai R. <kr...@Ce...>]

Hello Randy,

I have two suggestions for the mzData ontology. My first suggestion is th=
e
use of "instance_of". I think it would be more practical to define, for
example,
"Channeltron" as follows:
[Term]
id: PSI:1000107
name: Channeltron
def: ...
instance_of: PSI:1000026 ! DetectorType
I'm not saying that "is_a=10" is wrong in this and other cases, but
considering this snippet of XML (addmittedly a bit silly):
<detector>
<cvParam cvLabel=3D"psi" accession=3D"PSI:1000026" name=3D"mzOntology"
value=3D"DetectorType"/>
</detector>
a program would validate this a correct use of the ontology (unless
additional "intelligence" is programmed into it).
This leads me to another problem:
<source>
<cvParam cvLabel=3D"psi" accession=3D"PSI:1000026" name=3D"mzOntology"
value=3D"DetectorType"/>
</source>
is also quite difficult to spot as incorrect, as the ontology doesn't
define where the terms can be used. The use of "part_of" could resolve
this:
[Term]
id: PSI:1000026
name: DetectorType
def: ...
part_of: PSI:... ! Detector

Regards
 Kai

Randy Julian wrote:
> There is a new PSI Ontology File (for use with mzData) on the docstore:
>
> http://psidev.sourceforge.net/docstore/view.php?sess=3D0&parent=3D7&exp=
and=3D1&order=3Dname&sortname=3DASC&id=3D53&action=3Dfile_details
>
> There have been no new terms added (there are 204 entries).  But there
is now a definition section for every term, and the MS group is
> currently editing definitions.  Have a look and send any comments you h=
ave.
>
> The file can be viewed and edited in the beta version of the OBO-Edit
program:
>
> http://sourceforge.net/project/showfiles.php?group_id=3D36855&package_i=
d=3D148487
>
> or you can use a text editor...
>
> The next step is to reconcile the ontology with the second draft of the
IUPAC nomenclature (2006 draft):
>
> http://www.msterms.com/wiki/index.php?title=3DIUPAC_Task_Group_MS_Terms=
_Second_Draft
>
> There are terms which are needed by mzData and analysisXML which are no=
t
on this list, so any other instrument or data processing parameters
which are desired by the PSI membership can be send to Randy
> (rkj...@in...) or any other PSI-MS group member.
>
> The goal of the PSI-MS group is to update this file frequently, with th=
e
possibility of the human readable text changing to correct spelling or
to adjust to IUPAC norms, but the accession number assigned to the
concept is fixed and will not be changed, removed or reused.
>
> Thanks,
> Randy Julian
>
>
>
>
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--
Real cats don't need names.
But they often get called them.
"Yaargeroffoutofityarbastard" does nicely.
        Terry Pratchett - The Unadulterated Cat

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