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

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Hi

this was mentioned in a call last week and is also needed for MO. I 
think we will need some guidelines on this,

cheers

Helen

frank gibson wrote:
> 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... 
> <mailto: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...>
>     >>> [mailto: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... <mailto:sc...@eb...>
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>     > Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
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>     >
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>     <http://www.ebi.ac.uk/net-project>
>     >
>     > Personal
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>     >
>     >
>     >
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-- 
Helen Parkinson, PhD
Curation Coordinator
Microarray Informatics Team, 
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi