Re: [Psidev-ms-dev] [Obi-devel] Instrument Branch Scope and PSI instrument terms

[Daniel S. <sc...@eb...>]

Hello Stefan, OBI developers and PSI MS developers.
Yes, the OBI instrument branch  will have to review PSI term definitions 
for scope and applicability in OBI. Keep in mind that the PSI artifacts 
are less formal CVs and were mostly created in 'xml style'. That is why 
their graph/taxonomy is often 'xmlienated' (build using is-a _and_ 
part-of relations in one hierarchy). Their CVs also do not use any top 
level ontology and they sometimes have terms from the epistemiological 
level as part of their compound term names, e.g. Detector _Type_ and 
Analyzer _Description_. Sometimes they are not really explicit, using 
'ellipses' for term names, e.g. 'secondary electron' is_a 'detector 
type'. It should be  'secondary electron detector' is_a 'detector' instead.
But they concentrate on their domain only and have a specific 
application in mind. They never claimed to be fully ontological in the 
first place. All that lead them to be very narrowing in their 
definitions sometimes. So, Stefan is right. In many cases we have to 
refine the definitions and render them applicable in a more general way 
and e.g. a 'detector' class would be defined more broadly, and would 
probably get a mass_spectroscopy_detector subclass with would correspond 
to the MS 'detector'.
I assume that some of these glitches will vanish once the PSI design 
principles document ( including the naming conventions, 
http://www.psidev.info/index.php?q=node/100 ) will be approved and 
applied within PSI.

Best regards,
       Daniel Schober.

Stefan Wiemann wrote:

>I have had a look at the PSI_MS-InstrumentTermsForOBI file.
>This contains <term names> that are quite common also in other communities,
>however used there in a different sense. For example, the term <Accuracy> is
>defined as the "Accuracy of mass assignment", the term <Chromatography> as
>"Chromatographic conditions used to obtain the sample". I feel that this
>narrow definition of some terms might cause problems as the same terms may
>be used with a wider focus in other communities (Accuracy could also be the
>accuracy of a very different measurement, chromatography can be purely
>analytical). A <detector type> characterizes also the data acquisition
>mechanism in a video microscope, a FACS, or a plate reader. How is this
>terminology dealt with in OBI?
>Stefan
>
>  
>
>>-----Original Message-----
>>From: obi...@li... 
>>[mailto:obi...@li...] On Behalf Of 
>>Trish Whetzel
>>Sent: Tuesday, March 20, 2007 12:55 AM
>>To: OBI Developers
>>Subject: [Obi-devel] Instrument Branch Scope
>>
>>Just a quick note,  those on the Instrument Branch call last week 
>>decided that for terms such as petri dish, gel tank, cage 
>>etc. that we 
>>would like to collect these terms and work out a location for 
>>them in OBI. 
>>If your community has these kinds of terms, please post a 
>>tab-delimited 
>>file at:
>>https://www.cbil.upenn.edu/obiwiki/index.php/InstrumentTerms
>>containing the term name, definition and other Mandatory 
>>metadata items as 
>>listed on the wiki:
>>https://www.cbil.upenn.edu/obiwiki/index.php/WorkshopMetadata
>>
>>For those on that call, if have have missed any other important 
>>information for this item, please add.
>>
>>Trish
>>
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-- 
_______________________________________________________________________________________

Dr. Daniel Schober

NET Project - Ontologist

The European Bioinformatics Institute   email:  sc...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494410
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
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