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Re: [Psidev-ms-dev] [Obi-devel] Instrument Branch Scope and PSI instrument terms
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From: Chris T. <chr...@eb...> - 2007-03-20 12:08:28
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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 >>> >>> -------------------------------------------------------------- >>> ----------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the >>> chance to share your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge >>> >> &CID=DEVDEV >> >>> _______________________________________________ >>> Obi-devel mailing list >>> Obi...@li... >>> https://lists.sourceforge.net/lists/listinfo/obi-devel >>> >>> >> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Obi-devel mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-devel >> > > -- > _______________________________________________________________________________________ > > 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/ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://mibbi.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
