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

[Eric D. <ede...@sy...>]

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

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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?

- 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

- 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

- 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.

- 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:

- 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

- 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?