Re: [Psidev-ms-dev] new instrument CV terms

[David O. <do...@eb...>]

Hi all again,

New version of the controlled vocabulary: 3.7.3
"MassLynx"(MS:1000534) linked to "Waters software" (Waters software) and 
cv terms sorted in the obo file.

Best,
David

On 12/07/2011 16:49, David Ovelleiro wrote:
> 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
>>>>
>>>> ===========================================================
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>>>> Access to this email by anyone else is unauthorized and therefore prohibited. If you are
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>>>> ===========================================================
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>>
>>>>
>>>>
>>>> --
>>>> 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