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Re: [Psidev-ms-dev] new instrument CV terms
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From: David O. <do...@eb...> - 2011-07-12 15:49:33
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Hi Matt and community, In first place, thank you Matt for deleting the duplicated software, MassLynx. I did a quick check and it wasn't inside Waters software (in the next update, I'll quickly add the connection to Waters). Under "mass spectrometer" we have a mix of mass spectrometry techniques/methods and instruments... even something called "mass spectrometry/mass spectrometry". But, again, if someone is planning to use the "mass spectrometer" terms (and people from Waters seem to be doing so), I think is reasonable to re-locate this. Matt, please: don't touch the sorting of the file: I'm trying to reproduce the way Obo-Edit works. I've posted this afternoon an email in their email list about the way the application works for new IDs (the lastID variable doesn't seem to work any more). I'll keep you all informed. Anyway, I'm reporting in every new update the terms added (MS:1001797 the last one). Best, David On 12/07/2011 15:57, Matthew Chambers wrote: > I deleted the MassLynx term, it was a duplicate. I call it a "speedy delete"...it never happened! :P > > I was preparing an email to send yesterday including that tidbit but didn't finish it. Another thing > I was going to mention is that "TWIMS" should be "travelling wave ion mobility spectrometer" and > that it's awkward for IMS to be under "mass spectrometer" as you've mentioned below. Incidentally, > there is no mapping in the PSI formats for the "mass spectrometer" terms and its children. A lot of > the terms are still in purgatory simply because there isn't a need for them in the files. If we > wanted to go more in the direction of an ontology, we could associate each instrument with its > supported spectrometry methods. But that would require considerable discussion and work for little gain. > > Also I'm not sure about this inserting new terms into the middle of the OBO. It may be valid OBO but > it's rather confusing. I tend to make small additions with a text editor (after running them by the > list) so having new terms in the middle would make it easy to choose a duplicate accession. Is it > alright if I move the new terms to the bottom? I wouldn't expect it to need a version bump since it > doesn't change anything. > > -Matt > > > On 7/12/2011 5:16 AM, David Ovelleiro wrote: >> Dear Hans, Matt, Eric and PSI community, >> >> Empower, MassLynx and Unify and TWIMS have been included in the v.3.7.2 release of the psi-ms. ( >> v.3.7.1 had a small typo... sorry....) >> I think that with this, we've finished the list of terms proposed by Hans. I expect everything is >> fine.... if it's not... please, send an email. >> >> Dear Eric: thanks for the explanation. I was aware of the motivations for including some terms >> inside "purgatory". My concern is related to the fact that, if people is suggesting terms inside >> this "purgatory", maybe they are planning to use them. An xpath containing the word "purgatory" is, >> in my opinion, not very self-explanatory. >> To organize this, I'd propose changing the name of MS:1000293 (mass spectrometer) to "mass >> spectrometry methods" (I'm not sure this is the perfect name, but I suggest it because some of the >> patents related to them are named as "methods", e.g. http://www.freepatentsonline.com/7071465.html). >> We could then re-map MS:1000293 as son of "instrument" (MS:1000463). Only a suggestion... please, >> I'd like to hear some opinions. >> >> Best, >> David >> >> >> >> >> >> On 11/07/2011 17:25, Eric Deutsch wrote: >>> Hi David, thanks, these new terms look good to me. >>> >>> Regarding “mass spectrometry” and “purgatory”, please recall that “purgatory” is a ratty box of >>> terms that we just haven’t made a decision on yet. We don’t **want** and terms in “purgatory”, but >>> in a world of limited time, there they lie. In the CV, we are currently using “instrument” in lieu >>> of “mass spectrometer”. Why the term “mass spectrometer” is in purgatory I’m not quite certain. I >>> suppose it should just be obsoleted and make it a synonym of “instrument”. But I have a vague >>> recollection that we decided on “instrument” because some of these instruments have additional >>> components that are not strictly mass spectrometers (e.g. UV detection components). In which case, >>> there may be no role for a pure mass spectrometer. But maybe we couldn’t all agree on what to do, >>> so it lies in “purgatory” until the day that someone comes to decide and save the day. >>> >>> Regards, >>> >>> Eric >>> >>> *From:*David Ovelleiro [mailto:do...@eb...<mailto:do...@eb...>] >>> *Sent:* Monday, July 11, 2011 9:02 AM >>> *To:* Han...@wa...<mailto:Han...@wa...> >>> *Cc:* Mass spectrometry standard development >>> *Subject:* Re: [Psidev-ms-dev] new instrument CV terms >>> >>> Dear Hans, Matt and PSI community, >>> >>> I've updated the psi-ms c.v. with the 32 new Waters instruments list. >>> I'll also add, in a couple of days, the next 4 c.v. terms. Please, check them and if you see >>> anything wrong, write an email.... >>> >>> [Term] >>> id: MS:XXXXXXX >>> name: MassLynx >>> def: "Waters software for Mass spectrometry acquisition, processing and data analysis." [PSI:MS] >>> is_a: MS:1000694 ! Waters software >>> is_a: MS:1001456 ! analysis software >>> is_a: MS:1001457 ! data processing software >>> >>> [Term] >>> id: MS:XXXXXXX >>> name: Empower >>> def: "Waters software for liquid chromatography acquisition, processing, data analysis and data >>> management." [PSI:MS] >>> is_a: MS:1000694 ! Waters software >>> is_a: MS:1001456 ! analysis software >>> is_a: MS:1001457 ! data processing software >>> >>> [Term] >>> id: MS:XXXXXXX >>> name: Unify >>> def: "Waters software for liquid chromatography and mass spectrometry acquisition, processing, >>> data analysis and data management." [PSI:MS] >>> is_a: MS:1000694 ! Waters software >>> is_a: MS:1001456 ! analysis software >>> is_a: MS:1001457 ! data processing software >>> >>> >>> ********************************** New type of mass spectrometer, TWIMS ,son of IMS >>> >>> >>> id: MS:XXXXXXX >>> name: Travelling wave ion mobility mass spectrometer >>> def: "An ion mobility mass spectrometry technique based on the superimposition of travelling >>> voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS] >>> synonym: "TWIMS" EXACT [] >>> is_a: MS:1000261 ! ion mobility spectrometry >>> >>> >>> By the way... the "mass spectrometer" term (MS:1000293), is inside the purgatory... Do you >>> (community) really think this is the place for this term? Maybe is not used in the cv mappings for >>> mzML, but, anyway.... is strange, at least for me, finding the "mass spectrometer" in the purgatory... >>> >>> Best, >>> David >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 11/07/2011 07:28, Han...@wa...<mailto:Han...@wa...> wrote: >>> >>> Dear David and Matt, >>> >>> I have provided answers 'in line' in red. >>> >>> I will try to find out, with regard to Matt's question, if the instrument type can be retrieved >>> from the header.txt file. The serial number, i.e. JAA143, refers to a specific type and >>> configuration so this may be the easiest way forward. If an overview 'lookup type' table exists, I >>> will forward it. >>> >>> Would you happen to know who could be contacted for column liquid chromatography and sample >>> preparation CV terms? We are trying to integrate those as well into sample forms and a repository >>> like system, but finding them is not that straightforward. >>> >>> Thanks and best regards, >>> Hans >>> >>> >>> >>> >>> Inactive hide details for "David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for sending >>> us that intensive list of te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for >>> sending us that intensive list of terms. >>> >>> From: "David Ovelleiro"<do...@eb...> <mailto:do...@eb...> >>> To: "Mass spectrometry standard development"<psi...@li...> >>> <mailto:psi...@li...> >>> Cc: Han...@wa...<mailto:Han...@wa...> >>> Date: 08/07/2011 16:45 >>> Subject: Re: [Psidev-ms-dev] new instrument CV terms >>> >>> ---------------------------------------------------------------------------------------------------- >>> >>> >>> >>> >>> Dear Hans, >>> >>> Thanks for sending us that intensive list of terms. >>> >>> Some comments addressed to you and the rest of the community: >>> >>> 1. Instrument list >>> =============== >>> You’ve provided a list of 32 new instruments to be added. >>> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every new term will be like: >>> id: MS:XXXXXXX >>> name: Xevo TQ-S >>> def: "Waters quadrupole based instrument." [PSI:MS] >>> is_a: MS:1000126 ! Waters instrument model >>> >>> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied correctly in each case. Is this OK? >>> >>> b/ Some of the new proposed instruments maybe overlap with some of the old ones. I list below the >>> four “suspects” (old terms below “Waters instrument model” MS:1000126): >>> Acquity UPLC FLR >>> Acquity UPLC PDA >>> GCT >>> quattro micro >>> Please Hans, check if your new terms can safely be included without repeating some of the four >>> previous members. >>> >>> [HV]: >>> >>> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a fluorescence and PDA detector for >>> 'ACQUITY UPLC' liquid chromatography systems. >>> >>> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo TQD' mass spectrometers >>> >>> I therefore do not believe that there is CR term overlap/conflicts >>> >>> >>> >>> 2. Mass spectrometer >>> ================== >>> You propose a new “mass spectrometer type” called “Travelling wave mobility separator”. >>> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)? >>> b/ Is not more appropriate to use “Travelling wave ion mobility mass spectrometer” as the name of >>> the new cv term? >>> c/ Can we use Synonym: TWIMS? >>> d/ We would need a short description of the new kind of mass spectrometer. I’ve found this: “An >>> ion mobilitymass spectrometry technique based on the superimposition of travelling voltage waves >>> on a radially-confining RF voltage in agas-filled,stacked-ring ion guide”. Any better suggestion? >>> >>> [HV]: >>> >>> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant) >>> d/ see suggestion above >>> >>> >>> 3. Software >>> =========== >>> Three new “software” terms to be included: MassLynx, Empower and Unify. All three under “Waters >>> software” (MS:1000694). >>> a/ Please, Hans, we would need a short description of what these software do (one line each is >>> enough). >>> >>> [HV]: >>> >>> MassLynx: >>> "Mass spectrometry acquisition, processing and data analysis software" >>> >>> >>> Empower: >>> "Liquid chromatography acquisition, processing, data analysis and data management software" >>> >>> If believe that most vendors would call this CDS (chromatography data software). Would there be a >>> specific PSI-MS CV term for this? >>> >>> >>> Unify: >>> "Liquid chromatography and mass spectrometry acquisition, processing, data analysis and data >>> management software" >>> >>> >>> >>> I’ll be waiting for your comments, suggestions, changes, corrections… >>> >>> Best >>> david ovelleiro >>> >>> >>> >>> On 07/07/2011 09:05, Han...@wa...<mailto:Han...@wa...>wrote: >>> >>> >>> Dear all, >>> >>> Can the following instruments be added to the CV: >>> >>> quadrupole based: >>> >>> Xevo TQ-S >>> Xevo TQ MS >>> Xevo TQD >>> Acquity TQD >>> Acquity SQD >>> 3100 >>> Quattro micro GC >>> >>> oa-ToF based: >>> >>> Synapt G2-S HDMS >>> Synapt G2 HDMS >>> Synapt HDMS >>> Synapt G2-S MS >>> Synapt G2 MS >>> Synapt MS >>> MALDI Synapt G2-S HDMS >>> MALDI Synapt G2 HDMS >>> MALDI Synapt HDMS >>> MALDI Synapt G2-S MS >>> MALDI Synapt G2 MS >>> MALDI Synapt MS >>> Xevo G2 Q-Tof >>> Xevo Q-Tof >>> Xevo G2 Tof >>> GCT Premier >>> >>> LC-systems: >>> >>> ACQUITY UPLC I-Class >>> ACQUITY UPLC >>> ACQUITY UPLC H-Class >>> ACQUITY UPLC H-Class Bio >>> ACQUITY UPLC Systems with 2D Technology >>> nanoACQUITY UPLC >>> nanoACQUITY UPLC System with Technology >>> nanoACQUITY UPLC with HDX Technology >>> TRIZAIC UPLC nanoTile >>> >>> software: >>> >>> MassLynx >>> Empower >>> Unify >>> >>> mass spectrometer type: >>> >>> travelling wave mobility separator >>> >>> >>> The vendor or brand should be listed as "Waters Corporation". Would any more information be required? >>> >>> Thanks and best regards, >>> >>> Hans >>> >>> =========================================================== >>> The information in this email is confidential, and is intended solely for the addressee(s). >>> Access to this email by anyone else is unauthorized and therefore prohibited. If you are >>> not the intended recipient you are notified that disclosing, copying, distributing or taking >>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful. >>> =========================================================== >>> >>> >>> ------------------------------------------------------------------------------ >>> All of the data generated in your IT infrastructure is seriously valuable. >>> Why? It contains a definitive record of application performance, security >>> threats, fraudulent activity, and more. Splunk takes this data and makes >>> sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-d2d-c2 >>> >>> >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li...<mailto:Psi...@li...> >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> >>> >>> >>> -- >>> David Ovelleiro >>> Bioinformatician >>> PRIDE Group >>> Proteomics Services Team, PANDA Group >>> EMBL European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge, UK >>> CB10 1SD >>> >>> =========================================================== >>> The information in this email is confidential, and is intended solely for the addressee(s). >>> Access to this email by anyone else is unauthorized and therefore prohibited. If you are >>> not the intended recipient you are notified that disclosing, copying, distributing or taking >>> any action in reliance on the contents of this information is strictly prohibited and may be unlawful. >>> =========================================================== >>> >>> >>> >>> >>> -- >>> David Ovelleiro >>> Bioinformatician >>> PRIDE Group >>> Proteomics Services Team, PANDA Group >>> EMBL European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge, UK >>> CB10 1SD >>> >>> >>> ------------------------------------------------------------------------------ >>> All of the data generated in your IT infrastructure is seriously valuable. >>> Why? It contains a definitive record of application performance, security >>> threats, fraudulent activity, and more. Splunk takes this data and makes >>> sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-d2d-c2 >>> >>> >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> >> -- >> David Ovelleiro >> Bioinformatician >> PRIDE Group >> Proteomics Services Team, PANDA Group >> EMBL European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge, UK >> CB10 1SD >> >> >> >> ------------------------------------------------------------------------------ >> All of the data generated in your IT infrastructure is seriously valuable. >> Why? It contains a definitive record of application performance, security >> threats, fraudulent activity, and more. Splunk takes this data and makes >> sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-d2d-c2 >> >> >> >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- David Ovelleiro Bioinformatician PRIDE Group Proteomics Services Team, PANDA Group EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD |
