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Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT
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From: Pierre-Alain B. <pie...@is...> - 2007-04-20 16:16:50
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Yes, presumably. If it has to change for some reasons, we'll let you know. Pierre-Alain Trish Whetzel wrote: >> 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? >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------- >>>>> >>>>> >>>>> This SF.net email is sponsored by DB2 Express >>>>> Download DB2 Express C - the FREE version of DB2 express and take >>>>> control of your XML. No limits. Just data. Click to get it now. >>>>> http://sourceforge.net/powerbar/db2/ >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> 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 |
