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Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT
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From: Trish W. <wh...@pc...> - 2007-04-20 14:27:34
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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. 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