Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT

[Trish W. <wh...@pc...>]

> we can make a ccall from the main room. So let's say we'll use the usual
> numbers and codes (the same as for the WG ccalls)
> Talk to you soon
Excellent - will that be for both days?

Trish


>> Both of those times are fine with me as well.
>>
>> Trish
>>
>>> I am fine with both timings. Lyon time is 9 hours ahead of PDT.
>>> Please let me know the conf call number and such.
>>>
>>> Have a good time in Lyon,
>>>
>>>
>>> Pete.
>>>
>>>
>>> Eric Deutsch wrote:
>>>>
>>>> Hi everyone, here is a summary of discussion on the CV at today's call:
>>>>
>>>> At the end of the call, we discussed the possibility of having Trish
>>>> and Pete (who cannot attended Lyon) (and possibly others) be on a
>>>> conference call for selected times during the meeting, specifically
>>>>
>>>> - Monday 4:30p -- 6:00p Lyon time for full CV session
>>>>
>>>> - Tuesday 5:00p -- 6:00p Lyon time for final MS CV discussion
>>>>
>>>> Can this be arranged at the Lyon facilities?
>>>>
>>>> Terms that need debate:
>>>>
>>>> - msLevel - The term appears as Precursor Ion Scan (PSI:1000100),
>>>> Product Ion Scan (PSI:1000101) and Nth Generation Product Ion
>>>> (PSI:1000337). What term should we use for ms 4th, ms 5th and such?
>>>> We have to keep precursor ion and product ion. Terms such as
>>>> daughter ion and parent ion are deprecated. We still use Fragment
>>>> ion though. These are some additional related terms that I could
>>>> find in the CV.
>>>>
>>>> Both mzXML and mzData had a "msLevel" **attribute**. The decision
>>>> was made to put msLevel as a CV term in dataXML.  However, if we add
>>>> msLevel, it appears there would be some redundancy with existing
>>>> terms in the CV (as above). Decide how to proceed in Lyon.
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000364
>>>>
>>>> name: Fragment Ion
>>>>
>>>> def: "A product ion resulting from the dissociation of a precursor
>>>> ion." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000365 ! Ion
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000344
>>>>
>>>> name: Progeny Ion
>>>>
>>>> def: "A charged product of a series of consecutive reactions that
>>>> includes product ions, 1st generation product ions, 2nd generation
>>>> product ions, etc. Given the sequential fragmentation scheme: M1+ ?
>>>> M2+ ? M3+ ? M4+ ? M5+ M4+ is the precursor ion of M5+, a 1st
>>>> generation product ion of M3+, a 2nd generation product ion of M2+
>>>> and a 3rd generation product ion of M1+. " [PSI:GPS]
>>>>
>>>> exact_synonym: "Progeny Fragment Ion" []
>>>>
>>>> is_a: PSI:1000365 ! Ion
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000342
>>>>
>>>> name: Product Ion
>>>>
>>>> def: "An ion formed as the product of a reaction involving a
>>>> particular precursor ion. The reaction can unimolecular
>>>> dissociation, an ion/molecule reaction, or involve simply a change
>>>> in the number of charges. The terms daughter ion and parent ion are
>>>> not recommended." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000365 ! Ion
>>>>
>>>>
>>>>
>>>> - mzRangeStart, mzRangeStop
>>>>
>>>> According to Eric it would be useful to have a start and stop rather
>>>> than a single mass range which can be confusing. I think we need all
>>>> three terms: mass range, mzRangeStart and mzRangeStop. Is there
>>>> anyway to do that?
>>>>
>>>> Keep them as attributes instead? Discuss more in Lyon. Both previous
>>>> formats had them as separate attributes, not CV terms.
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000313
>>>>
>>>> name: Mass Range
>>>>
>>>> def: "The limit of m/z over which a mass spectrometer can detect
>>>> ions." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000444 ! m/z Separation Method
>>>>
>>>>
>>>> - I dont know what is this term for?:
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000104
>>>>
>>>> name: None
>>>>
>>>> def: "None." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000021 ! Reflectron State
>>>>
>>>> History of this term unknown.  Maybe Randy knows? Eric will ask him.
>>>>
>>>> - Instrument Name
>>>>
>>>> i think Instrument name is same as model because Instrument's model
>>>> name is everything but the Vendor's name. Also, each instrument will
>>>> be defined, such as LTQ-FT LTQ Orbitrap. The definition of each
>>>> model would contain the vendor name. That means we are keeping Model
>>>> as it is and Instrument Name will not be used?
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000463
>>>>
>>>> name: Instrument
>>>>
>>>> def: "Device which performs a measurement." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000031
>>>>
>>>> name: Model
>>>>
>>>> def: "Instrument's model name (everything but the vendor's name)"
>>>> [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:1000454 ! Instrument Additional Description
>>>>
>>>> Use the term "InstrumentModel" and not "InstrumentName" or "Model"
>>>>
>>>> Maybe make new term "InstrumentModel" and deprecate "Model" and will
>>>> not use "InstrumentName"
>>>>
>>>> Bring up in Lyon, to find out what the recommendation is for tidying
>>>> up the ontology.
>>>>
>>>> - Should we replace all ThermoFinnigan with Thermo Fisher Scientific
>>>> because the company name has changed?
>>>>
>>>> Create a new vendor term "Thermo Fisher Scientific" instead of
>>>> renaming previous one.  The vendor for many existing years-old mass
>>>> specs was ThermoFinnigan at the time.  Maybe putting a date range in
>>>> the definitions would be helpful?
>>>>
>>>> - LowestMzValue - Is this within a spectrum or within a experiment.
>>>> A clear definition is needed.
>>>>
>>>> - HighestMzValue - Again what is the reference for this term. I have
>>>> to know what is it for in order                    to get a clear
>>>> definintion. Lowest and highest observed values in a spectrum. Used
>>>> by some software instead of opening up all spectra.
>>>>
>>>> - Scan Type - "Dictates the type of scan used to generate the
>>>> spectrum. Usually refers to the range but can also include linked,
>>>> precursor, product and neutral mass loss types of scan."
>>>>
>>>> What is the difference between Scan Type and Scan Mode?
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000036
>>>>
>>>> name: Scan Mode
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_obsolete: true
>>>>
>>>> Pete will research this more and report back.
>>>>
>>>> Try to get Trish and Pete to the Monday 4:30 -- 6:00, and maybe
>>>> Tuesday 5:00 -- 6:00p
>>>>
>>>> Lyon is currently GMT+2
>>>>
>>>> Encourage vendors to enter items via the term tracker including
>>>> definitions
>>>>
>>>> Eric will email Pierre-Alain and others about joining in on Monday,
>>>> Tuesday
>>>>
>>>> Terms to be added:
>>>>
>>>>
>>>> - We need to add:  LCQ Deca and LCQ Deca XP. Others are there.
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000169
>>>>
>>>> name: LCQ Deca XP Plus
>>>>
>>>> def: "ThermoFinnigan LCQ Deca XP Plus MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000168
>>>>
>>>> name: LCQ Classic
>>>>
>>>> def: "ThermoFinnigan LCQ Classic MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000167
>>>>
>>>> name: LCQ Advantage
>>>>
>>>> def: "ThermoFinnigan LCQ Advantage MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>>
>>>> - Add InstrumentSerialNumber as a term. We are not using
>>>> InstrumentIdentifier because serial number is unique.
>>>>
>>>> Okay.
>>>>
>>>> - Add -FileFormatConversion as a term.
>>>>
>>>> Used, e.g., to describe how ReAdW converts RAW to dataXML
>>>>
>>>> - MaldiSpotIdentifier - sample spot, analyte spot or MALDIspot would
>>>> be a better term.
>>>>
>>>>
>>>> Terms whose definitions needs to be updated:
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000441
>>>>
>>>> name: Scan
>>>>
>>>> def: "A function of the mass spectrometer in which it employs the
>>>> mass analyzer to generate the mass spectrum of a range of ions or a
>>>> specific ion" [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000036
>>>>
>>>> name: Scan Mode
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_obsolete: true
>>>>
>>>> -DataArrayContentType
>>>>
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000139
>>>>
>>>> name: 4000 Q TRAP
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000140
>>>>
>>>> name: 4700 Proteomic Analyzer
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX 4700 Proteomic Analyzer MS"
>>>> [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000141
>>>>
>>>> name: APEX IV
>>>>
>>>> def: "Bruker Daltonics APEX IV MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000142
>>>>
>>>> name: APEX-Q
>>>>
>>>> def: "Bruker Daltonics APEX-Q MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000143
>>>>
>>>> name: API 150EX
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX API 150EX MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000144
>>>>
>>>> name: API 150EX Prep
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000145
>>>>
>>>> name: API 2000
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX API 2000 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000146
>>>>
>>>> name: API 3000
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX API 3000 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000147
>>>>
>>>> name: API 4000
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX API 4000 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000148
>>>>
>>>> name: autoFlex II
>>>>
>>>> def: "Bruker Daltonics autoFlex II MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000149
>>>>
>>>> name: autoFlex TOF/TOF
>>>>
>>>> def: "Bruker Daltonics autoFlex TOF/TOF MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000150
>>>>
>>>> name: Auto Spec Ultima NT
>>>>
>>>> def: "Waters AutoSpec Ultima NT MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000151
>>>>
>>>> name: Bio TOF II
>>>>
>>>> def: "Bruker Daltonics BioTOF II MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000152
>>>>
>>>> name: Bio TOF Q
>>>>
>>>> def: "Bruker Daltonics BioTOF Q MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000153
>>>>
>>>> name: DELTA plusAdvantage
>>>>
>>>> def: "ThermoFinnigan DELTAplusAdvantage MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000154
>>>>
>>>> name: DELTAplusXP
>>>>
>>>> def: "ThermoFinnigan DELTAplusXP MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000155
>>>>
>>>> name: ELEMENT2
>>>>
>>>> def: "ThermoFinnigan ELEMENT2 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000156
>>>>
>>>> name: esquire4000
>>>>
>>>> def: "Bruker Daltonics esquire4000 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000157
>>>>
>>>> name: esquire6000
>>>>
>>>> def: "Bruker Daltonics esquire6000 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000158
>>>>
>>>> name: Explorer
>>>>
>>>> def: "IonSpec Explorer MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000159
>>>>
>>>> name: GCT
>>>>
>>>> def: "Waters GCT MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000160
>>>>
>>>> name: HCT
>>>>
>>>> def: "Bruker Daltonics HCT MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000161
>>>>
>>>> name: HCT Plus
>>>>
>>>> def: "Bruker Daltonics HCTPlus MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000162
>>>>
>>>> name: HiRes ESI
>>>>
>>>> def: "IonSpec HiResESI MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000163
>>>>
>>>> name: HiRes MALDI
>>>>
>>>> def: "IonSpec HiResMALDI MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000164
>>>>
>>>> name: IsoPrime
>>>>
>>>> def: "Waters IsoPrime MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000165
>>>>
>>>> name: IsoProbe
>>>>
>>>> def: "Waters IsoProbe MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000166
>>>>
>>>> name: IsoProbe T
>>>>
>>>> def: "Waters IsoProbe T MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000167
>>>>
>>>> name: LCQ Advantage
>>>>
>>>> def: "ThermoFinnigan LCQ Advantage MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000168
>>>>
>>>> name: LCQ Classic
>>>>
>>>> def: "ThermoFinnigan LCQ Classic MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000169
>>>>
>>>> name: LCQ Deca XP Plus
>>>>
>>>> def: "ThermoFinnigan LCQ Deca XP Plus MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000170
>>>>
>>>> name: M@LDI L
>>>>
>>>> def: "Waters M@LDI L MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000171
>>>>
>>>> name: M@LDI LR
>>>>
>>>> def: "Waters M@LDI LR MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000172
>>>>
>>>> name: MAT253
>>>>
>>>> def: "ThermoFinnigan MAT253 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000173
>>>>
>>>> name: MAT900XP
>>>>
>>>> def: "ThermoFinnigan MAT900XP MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000174
>>>>
>>>> name: MAT900XP Trap
>>>>
>>>> def: "ThermoFinnigan MAT900XP Trap MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000175
>>>>
>>>> name: MAT95XP
>>>>
>>>> def: "ThermoFinnigan MAT95XP MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000176
>>>>
>>>> name: MAT95XP Trap
>>>>
>>>> def: "ThermoFinnigan MAT95XP Trap MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000177
>>>>
>>>> name: microFlex
>>>>
>>>> def: "Bruker Daltonics microFlex MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000178
>>>>
>>>> name: microTOFLC
>>>>
>>>> def: "Bruker Daltonics microTOFLC MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000179
>>>>
>>>> name: Neptune
>>>>
>>>> def: "ThermoFinnigan NEPTUNE MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000180
>>>>
>>>> name: NG-5400
>>>>
>>>> def: "Waters NG-5400 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000181
>>>>
>>>> name: OMEGA
>>>>
>>>> def: "IonSpec OMEGA MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000182
>>>>
>>>> name: OMEGA-2001
>>>>
>>>> def: "IonSpec OMEGA-2001 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000183
>>>>
>>>> name: OmniFlex
>>>>
>>>> def: "Bruker Daltonics OminFlex MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000184
>>>>
>>>> name: Platform ICP
>>>>
>>>> def: "Waters Platform ICP MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000185
>>>>
>>>> name: PolarisQ
>>>>
>>>> def: "ThermoFinnigan PolarisQ MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000186
>>>>
>>>> name: Proteomics Solution 1
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000187
>>>>
>>>> name: Q TRAP
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX Q TRAP MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000188
>>>>
>>>> name: Q-Tof micro
>>>>
>>>> def: "Waters Q-Tof micro MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000189
>>>>
>>>> name: Q-Tof Ultima
>>>>
>>>> def: "Waters Q-Tof Ultima MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000190
>>>>
>>>> name: QSTAR
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX QSTAR MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000191
>>>>
>>>> name: Quattro micro
>>>>
>>>> def: "Waters Quattro micro MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000192
>>>>
>>>> name: Quattro UItima
>>>>
>>>> def: "Waters Quattro Uitima MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000193
>>>>
>>>> name: Surveyor MSQ
>>>>
>>>> def: "ThermoFinnigan Surveyor MSQ MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000194
>>>>
>>>> name: SymBiot I
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX SymBiot I MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000195
>>>>
>>>> name: SymBiot XVI
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000196
>>>>
>>>> name: TEMPUS TOF
>>>>
>>>> def: "ThermoFinnigan TEMPUS TOF MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000197
>>>>
>>>> name: TRACE DSQ
>>>>
>>>> def: "ThermoFinnigan TRACE DSQ MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000198
>>>>
>>>> name: TRITON
>>>>
>>>> def: "ThermoFinnigan TRITON MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000199
>>>>
>>>> name: TSQ QUANTUM
>>>>
>>>> def: "ThermoFinnigan TSQ QUANTUM MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000200
>>>>
>>>> name: Ultima
>>>>
>>>> def: "IonSpec Ultima MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000201
>>>>
>>>> name: ultraFlex
>>>>
>>>> def: "Bruker Daltonics ultraFlex MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000202
>>>>
>>>> name: ultraFlex TOF/TOF
>>>>
>>>> def: "Bruker Daltonics ultraFlex TOF/TOF MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000203
>>>>
>>>> name: Voyager-DE PRO
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000204
>>>>
>>>> name: Voyager-DE STR
>>>>
>>>> def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS" [PSI:GPS]
>>>>
>>>> is_a: PSI:1000031 ! Model
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000441
>>>>
>>>> name: Scan
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000442
>>>>
>>>> name: Spectrum
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000443
>>>>
>>>> name: Mass Analyzer
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000444
>>>>
>>>> name: m/z Separation Method
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000445
>>>>
>>>> name: Sequential m/z Separation Method
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000036
>>>>
>>>> name: Scan Mode
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_obsolete: true
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000127
>>>>
>>>> name: Centroid Mass Spectrum
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000035 ! Peak Processing
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000128
>>>>
>>>> name: Continuum Mass Spectrum
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000035 ! Peak Processing
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000131
>>>>
>>>> name: Number Of Counts
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000043 ! Intensity Unit
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000132
>>>>
>>>> name: Percent Of Base Peak
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000043 ! Intensity Unit
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000138
>>>>
>>>> name: Percent
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> is_a: PSI:1000046 ! Energy Unit
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000441
>>>>
>>>> name: Scan
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000442
>>>>
>>>> name: Spectrum
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000443
>>>>
>>>> name: Mass Analyzer
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000444
>>>>
>>>> name: m/z Separation Method
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>> [Term]
>>>>
>>>> id: PSI:1000445
>>>>
>>>> name: Sequential m/z Separation Method
>>>>
>>>> def: "TODO: Add definition." [PSI:GPS]
>>>>
>>>> relationship: part_of PSI:0000000 ! mzOntology
>>>>
>>>>
>>>>
>>>> Terms we decided not to add:
>>>>
>>>>
>>>> - AnalyteIdentifier - same as Sample Name (PSI:1000002), and/or Sample
>>>>
>>>> Number (PSI:1000001)
>>>>
>>>> - BasePeakMz - same as Base Peak, PSI:1000210
>>>>
>>>>
>>>> - InstrumentIdentifier. Same as InstrumentSerialNumber.
>>>>
>>>>
>>>> _____________________________________________
>>>> *From:* Eric Deutsch
>>>> *Sent:* Monday, April 16, 2007 8:05 PM
>>>> *To:* 'Pierre-Alain Binz'; 'Trish Whetzel'; 'Puneet Souda';
>>>> 'psi...@li...'
>>>> *Cc:* Eric Deutsch
>>>> *Subject:* RE: PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT
>>>>
>>>> Hi everyone, this is a reminder of the conference call Tuesday, 9am
>>>> PDT, 12n EDT, 4pm GMT. Agenda items are:
>>>>
>>>> - Review recent work on the CV (see attached list of items to
>>>> discuss from Pete)
>>>>
>>>> - Discuss required preparation for next week
>>>>
>>>>  << File: PSI_TermsReview_Merge.txt >>
>>>>
>>>> MS-WG ccall Tuesday, 9am PDT, 12n EDT, 4pm GMT
>>>>
>>>> - Phone numbers:
>>>>
>>>>   + Germany: 08001012079
>>>>
>>>>   + Switzerland: 0800000860
>>>>
>>>>   + UK: 08081095644
>>>>
>>>>   + USA: 1-866-314-3683
>>>>
>>>>   + Generic international: +44 2083222500 (UK number)
>>>>
>>>> access code: 297427
>>>>
>>>> Thanks,
>>>>
>>>> Eric
>>>>
>>>> _____________________________________________
>>>> *From:* Eric Deutsch
>>>> *Sent:* Monday, April 09, 2007 1:07 AM
>>>> *To:* 'Pierre-Alain Binz'; Trish Whetzel; Puneet Souda; Kent
>>>> Laursen; psi...@li...
>>>> *Cc:* Eric Deutsch
>>>> *Subject:* PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT
>>>>
>>>> Hi everyone, here is a summary of the issues before us regarding
>>>> dataXML. Please read it over and let's discuss at the conference
>>>> call on Tuesday. Call information:
>>>>
>>>> MS-WG ccall Tuesday, 9am PDT, 12n EDT, 4pm GMT
>>>>
>>>> - Phone numbers:
>>>>
>>>>   + Germany: 08001012079
>>>>
>>>>   + Switzerland: 0800000860
>>>>
>>>>   + UK: 08081095644
>>>>
>>>>   + USA: 18663143683
>>>>
>>>>   + Generic international: +44 2083222500 (UK number)
>>>>
>>>> access code: 297427
>>>>
>>>>
>>>> --------------------------------------------------------------------------------------------------
>>>>
>>>>
>>>> Open issues with dataXML
>>>>
>>>> - Need documentation of each element and attribute
>>>>
>>>>   Mike Coleman  2007-02-06
>>>>
>>>>   Agreed. Does Kent have some start of documentation from
>>>> current/previous XMLSpy docs?
>>>>
>>>> Eric will contact Kent directly
>>>>
>>>> - Need more specifics on the desired numerical formats (e.g., IEEE,
>>>> etc.)
>>>>
>>>>   Mike Coleman  2007-02-06
>>>>
>>>>   To be discussed in Lyon
>>>>
>>>> - Should there be "count" attributes?
>>>>
>>>>   Frederik Levander  2007-02-06
>>>>
>>>>   This is useful for some parsers. Probably leave in place. Discuss
>>>> in Lyon
>>>>
>>>> - Should file index be within the file or in a separate file?
>>>>
>>>>   Frederik Levander  2007-02-06
>>>>
>>>>   The implementation of dataXML to be presented at Lyon will include
>>>> this information in the same file. Further discussion deferred to
>>>> the Lyon meeting The question was there: Should the file name /
>>>> checksum information be held in a separate file?
>>>>
>>>> - Encoded filename should be element content instead of an
>>>> attribute, so that CDATA could be used
>>>>
>>>>   Alex Masselot  2007-02-07
>>>>
>>>>   To be discussed in Lyon
>>>>
>>>> - Should controlled vocabulary term values also be element content
>>>> instead of attribute so that CDATA could be used?
>>>>
>>>>   Alex Masselot  2007-02-07
>>>>
>>>>   To be discussed in Lyon
>>>>
>>>> - How will we handle multiple charges for parent peak, and
>>>> fragmentation peaks?
>>>>
>>>>   Alex Masselot  2007-02-07
>>>>
>>>>   This is already handled -- mutliple cvParams of the same type can
>>>> be used to annotate one peak / spectrum.
>>>>
>>>> - How can we allow two cv terms to be linked, such as concept with
>>>> value and the associated units (a separate cv term). (e.g.
>>>> "collision energy"=35.0 & "energy units"="joules")
>>>>
>>>>   Phil Jones  2007-02-27  (followup by Angel and Kent 02-28)
>>>>
>>>>   Phil to post to list for further responses
>>>>
>>>> Phil suggested 2 possibilities: <annotation> and additional attributes
>>>>
>>>> Angel suggested doing the FuGE way. Maybe overkill? Difficult for
>>>> software to handle?
>>>>
>>>> Do we really need having both or could we encode the units within
>>>> the terms, e.g. "collision energy in joules"
>>>>
>>>> Most other relevant CVs don't seem to encode units as part of the term
>>>>
>>>> Defer this to Lyon? Try to include the CV folks in a conference call
>>>> during meeting
>>>>
>>>> Do we need to have specific types of relationships between linked
>>>> terms, like "has_units"?
>>>>
>>>> - People still wrinkle their nose when hearing the "dataXML" name.
>>>> We have a suggestion on the floor to rename to "mzDataXML".  Comments?
>>>>
>>>> - Make sure dataXML web site is up to date as can be
>>>>
>>>> - DONE Add link to XMLSpy-generated documentation at:
>>>>
>>>>
>>>> _http://gelbank.anl.gov/schema/documentations/dataXML0.11/dataXML0.11.html_
>>>>
>>>>
>>>> - Get the indexing wrapper schema working properly
>>>>
>>>>   Jayson Falkner  2006-11-15
>>>>
>>>> - Make sure that Karl Klauser is invited to be involved
>>>>
>>>> Eric will send email.
>>>>
>>>> - Do we support properly the spectrum "library" use case?
>>>>
>>>>   Karl Klauser 2007-01-18
>>>>
>>>>   dataXML is supposed to be for MS instrument raw data, not
>>>> interpreted data, i.e. with assignments. That is what analysisXML is
>>>> intended for.
>>>>
>>>> Still open questions here. If analysisXML doesn't includes spectra,
>>>> this would be tricky.
>>>>
>>>> - Examine the mapping with MIAPE. Do we support everything MIAPE
>>>> requires?
>>>>
>>>>   Pierre-Alain Binz  2007-03-30
>>>>
>>>>   This will be addressed in Lyon
>>>>
>>>> - Revisit the chromatogram use case and develop a good example
>>>>
>>>>
>>>> Controlled Vocabulary Issues:
>>>>
>>>> Trish sent out a new version of the CV this morning.
>>>>
>>>> New terms from Dave Horn added
>>>>
>>>> Will start keeping and posting release notes
>>>>
>>>> Pete should start working on this new version now
>>>>
>>>> Pete, Trish, and I will iterate on CV a little and there will be
>>>> another ccall in 1 week exactly to discuss further
>>>>
>>>> We should post the OBO file soon on OBO.
>>>>
>>>> We will meet again in a week roughly, but Pete can't do next Tue 9am
>>>>
>>>> - DONE. Add hyperlink to the current CV on the web site
>>>>
>>>>   _http://psidev.sourceforge.net/ms/xml/mzdata/psi-ms-cv-latest.obo_
>>>>
>>>> - Should we change the ontology namespace to PSI-MS?
>>>>
>>>>   Trish Whetzel  2007-03-27
>>>>
>>>>   Was suggested in Washington already and we decided no?
>>>>
>>>> - What is the overlap/division between the PSI-MS CV, the main PSI
>>>> CV, OBI?
>>>>
>>>>   Trish Whetzel, Luisa Montecchi  2007-03-30
>>>>
>>>>   To be sorted out in a special working session in Lyon?
>>>>
>>>> - Should we even have an InstrumentIdentifier (local to lab) term at
>>>> all?
>>>>
>>>>   Trish Whetzel  2007-03-19
>>>>
>>>> - What is required from vendors?
>>>>
>>>>   Pierre-Alain  2007-04-03
>>>>
>>>> - How do we deal with the common PSI CV?
>>>>
>>>>   Pierre-Alain  2007-04-03
>>>>
>>>> - What is the overlap with OBO ontology "ProPreo"?
>>>>
>>>>   ProPreo: A comprehensive proteomics data and process provenance
>>>> ontology
>>>>
>>>>   _http://lsdis.cs.uga.edu/projects/glycomics/propreo/_
>>>>
>>>>   Eric Deutsch  2007-04-03
>>>>
>>>> Trish says there was a quick review of this ~ 8 months ago
>>>>
>>>> ProPreo is broader but not deep enough
>>>>
>>>> - Try to reconcile the latest instance document and the current PSI
>>>> ontology:
>>>>
>>>>   Trish Whetzel  2007-03-30
>>>>
>>>>   Eric Deutsch responded 2007-04-03
>>>>
>>>>   (full exchange not repro'ed here)
>>>>
>>>>   Pete or someone trying to resolve based on discussion thus far and
>>>> identify unresolved?
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> -------------------------------------------------------------------------
>>>>
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>>>>
>>>>
>>>> _______________________________________________
>>>> Psidev-ms-dev mailing list
>>>> Psi...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>>
>>
>
> -- 
> --
> Dr. Pierre-Alain Binz
> Swiss Institute of Bioinformatics
> Proteome Informatics Group
> 1, Rue Michel Servet
> CH-1211 Geneve 4
> Switzerland
> - - - - - - - - - - - - - - - - -
> Tel: +41-22-379 50 50
> Fax: +41-22-379 58 58
> Pie...@is...
> http://www.expasy.org/people/Pierre-Alain.Binz.html
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
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> _______________________________________________
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