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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 14:33:17
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Good, 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 Pierre-Alain Trish Whetzel wrote: > 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 |
