psidev-pi-dev

[Psidev-pi-dev] Reminder: TeleConference TODAY, June 5th, 2008

[Martin E. <mar...@ru...>]

Hi everyone,

there will be an AnalysisXML working
group conference call today (Thursday)
at 4 PM UK time:
http://www.timeanddate.com/worldclock/fi
xedtime.html?day=5&month=6&year=2008&hou
r=16&min=0&sec=0&p1=136


Minutes of last meeting at:
http://psidev.info/index.php?q=node/332


Agenda:
1. Review minutes of last meeting and
newest schema

2. Discuss cleavage agent settings and 
Continue with review of the Excel
spreadsheet to decide what needs to
be attributes and what needs to be CV. 
The spreadsheet:
http://code.google.com/p/psi-pi/source/b
rowse/trunk/cv/
 
3. if time: go through issues list
http://code.google.com/p/psi-pi/issues/l
ist


  Best regards
   Martin

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(UK number)

access code: 297427

[Psidev-pi-dev] Updated schema

[Jones, A. <And...@li...>]

Hi all,

I've made a few edits to the schema as discussed on the call, and tidied up the SVN, so the main working version is the only file in the schema directory. 

Changes:
-	Altered cardinality of AnalysisCollection and AnalysisProtocolCollection to 1, since I think it should not be possible to create a file without any protocols or protocol applications (as least if there is a protocol application there must be a protocol). Let me know if anyone disagrees and I'll change it back
-	Removed PolypeptideValuePropertyType and ValuePropertyType, Intensity, RetentionTime (think these were left over in the schema and not required)
-	Put the AnalysisXML complexType first in the schema to make it easier to find.
-	Worked thru schema and put in PropertyValue (value + unit + unitAccession) references instead of cvParam where sensible...
- 	Added the option for userParam or cvParam by adding an abstract ParamType (changed over most of the references to ParamType, although I may have missed a few)
-	Made TranslationTable cardinality 1, as suggested by Martin’s email

One minor problem. On the call we discussed using XSD style inheritance for cvParam, where an entity e.g. SearchType uses the cvParamType complexType. Unfortunately, this does not work with also using the other style of inheritance where you can give the option of a userParam or cvParam by giving a reference to an abstract superclass e.g. ParamType. 

So... we either go back to the old style of having e.g.

<SearchType>
	<cvParam ...>


Or we ditch the option of having cvParam or userParam as an option, and only user cvParam. We could for example make cvRef and accession optional, so a userParam is just a cvParam without the reference. I can give examples if I haven't explained this clearly enough.

Cheers
Andy

Re: [Psidev-pi-dev] Updated schema

[Jones, A. <And...@li...>]

And if Phil wants to send round a suggestion for fragment ions, I'll add this to the schema on Monday

> -----Original Message-----
> From: psi...@li... [mailto:psidev-pi-dev-
> bo...@li...] On Behalf Of Jones, Andy
> Sent: 06 June 2008 15:57
> To: psi...@li...
> Subject: [Psidev-pi-dev] Updated schema
> 
> Hi all,
> 
> I've made a few edits to the schema as discussed on the call, and tidied up the
> SVN, so the main working version is the only file in the schema directory.
> 
> Changes:
> -	Altered cardinality of AnalysisCollection and AnalysisProtocolCollection to
> 1, since I think it should not be possible to create a file without any protocols or
> protocol applications (as least if there is a protocol application there must be a
> protocol). Let me know if anyone disagrees and I'll change it back
> -	Removed PolypeptideValuePropertyType and ValuePropertyType,
> Intensity, RetentionTime (think these were left over in the schema and not
> required)
> -	Put the AnalysisXML complexType first in the schema to make it easier to
> find.
> -	Worked thru schema and put in PropertyValue (value + unit +
> unitAccession) references instead of cvParam where sensible...
> - 	Added the option for userParam or cvParam by adding an abstract
> ParamType (changed over most of the references to ParamType, although I may
> have missed a few)
> -	Made TranslationTable cardinality 1, as suggested by Martin’s email
> 
> One minor problem. On the call we discussed using XSD style inheritance for
> cvParam, where an entity e.g. SearchType uses the cvParamType complexType.
> Unfortunately, this does not work with also using the other style of inheritance
> where you can give the option of a userParam or cvParam by giving a reference to
> an abstract superclass e.g. ParamType.
> 
> So... we either go back to the old style of having e.g.
> 
> <SearchType>
> 	<cvParam ...>
> 
> 
> Or we ditch the option of having cvParam or userParam as an option, and only
> user cvParam. We could for example make cvRef and accession optional, so a
> userParam is just a cvParam without the reference. I can give examples if I haven't
> explained this clearly enough.
> 
> Cheers
> Andy
> 
> 
> 
> 
> 
> 
> 
> 
> 
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