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

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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.=20

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.=20

- HighestMzValue - Again what is the reference for this term. I have to
know what is it for in order                    to get a clear
definintion. =20

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.=20

[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.=20

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=20
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 >>=20
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=20
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"=3D35.0 & "energy units"=3D"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:
=20
http://gelbank.anl.gov/schema/documentations/dataXML0.11/dataXML0.11.htm
l

- 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?