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Re: [Psidev-ms-dev] [Obi-devel] Instrument Branch Scope and PSI instrument terms
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From: frank g. <Fra...@nc...> - 2007-03-20 13:35:35
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Hi The next PSI meeting is due to be held on the 23-25th April. It would be great if something was prepared, even only for discussion, for this date. Cheers Frank On 3/20/07, Helen Parkinson <par...@eb...> wrote: > > 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 > > >>> > > >>> -------------------------------------------------------------- > > >>> ----------- > > >>> 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 > > <http://www.techsay.com/default.php?page=join.php&p=sourceforge> > > >>> > > >> &CID=DEVDEV > > >> > > >>> _______________________________________________ > > >>> Obi-devel mailing list > > >>> Obi...@li... > > <mailto: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 > > < > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> > > >> _______________________________________________ > > >> Obi-devel mailing list > > >> Obi...@li... > > <mailto:Obi...@li...> > > >> https://lists.sourceforge.net/lists/listinfo/obi-devel > > >> > > > > > > -- > > > > > > _______________________________________________________________________________________ > > > > > > > > Dr. Daniel Schober > > > > > > NET Project - Ontologist > > > > > > The European Bioinformatics Institute > > email: sc...@eb... <mailto: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 > > <http://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 > > < > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > Psidev-ms-dev mailing list > > > Psi...@li... > > <mailto:Psi...@li...> > > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~~ > > chr...@eb... <mailto:chr...@eb...> > > http://mibbi.sf.net/ <http://mibbi.sf.net/> > > ~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > ------------------------------------------------------------------------- > > 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 > > < > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> > > _______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... > > <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > > > > ------------------------------------------------------------------------ > > > > > ------------------------------------------------------------------------- > > 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 > > > > -- > Helen Parkinson, PhD > Curation Coordinator > Microarray Informatics Team, > EBI > > EBI 01223 494672 > Skype: helen.parkinson.ebi > > |
