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

[Puneet S. <ps...@ch...>]

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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