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

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Hi Pete,

Did you add terms to the OBO file? I did not see any new terms added to 
the tracker.

Is the list attached here a further review of the terms that I sent 
questions on or are there new terms included in this list? At first 
glance, I am not sure how this list relates to the list that I sent to you 
and Eric.

Thanks,
Trish

> 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
> <<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.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?
>
>
>
>