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

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Hi

I would also like to highlight, that if term definitions or hierarchies are
changed within OBI from the original CVs there needs to be some sort of
feedback or mapping presented back to the PSI. As Daniel points out these
exist for a particular purpose and for a particular community, if they dont
find the terms they expect in OBI then they wont use it. Hopefully this
feedback will also help develop more well designed CVs in the future.

Frank

On 3/20/07, Chris Taylor <chr...@eb...> wrote:
>
> Just in passing, its worth remembering also that (for example)
> the MS terms in OBI should also be amenable to use by
> metabolomics people, MS-based nucleotide sequencers, etc.
>
> I believe there is still a plan to 'flag' terms as appropriate
> to a particular domain (such as proteomics), but the use of
> omics-based conceptions of the world to shape the structure of
> the ontology is dysfunctional and won't feature in OBI per se.
>
> Cheers, Chris.
>
>
> Daniel Schober wrote:
> > 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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> >>>
> >>
> >>
> >>
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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
> > Cambridge CB10 1SD, UK                        Room: A2-37
> >
> > Project page: www.ebi.ac.uk/net-project
> >
> > Personal page:
> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> > Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
> >
> >
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> --
> ~~~~~~~~~~~~~~~~~~~~~~~~
>   chr...@eb...
>   http://mibbi.sf.net/
> ~~~~~~~~~~~~~~~~~~~~~~~~
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