Re: [Psidev-pi-dev] Changes to schema on 29th July 2008

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

Hi David, hi all!
 
Mh, I cannot find a MPC_use_case_working_temp.axml (where have you found it?); 
the latest is MPC_use_case_working27June.axml and it has no empty SearchDatabase_ref.
 
But I think SearchDatabase_ref should be optional in the <Inputs> because of non-database searches.
 
Andy added SearchDatabase_ref and accession into <DBSequence> and there it 
makes sense to make them mandatory (because it is “DB”sequence).
 
It would be more human-readable to have:
<SpectraData ref="SD_1"/>
<SearchDatabase ref="SDB_SwissProt"/>
but I agree with Andy it maybe more FuGe and more validatable to have
      <SpectraData SpectraData_ref="SD_1"/>
      <SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>


(For some seconds I thought to move them to attributes but we have potentially more than one.)
 
 Bye
   Martin
 
 
Von: psi...@li... [mailto:psi...@li...] Im Auftrag von David Creasy
Gesendet: Wednesday, July 30, 2008 6:00 AM
An: psi...@li...
Betreff: [Psidev-pi-dev] Changes to schema on 29th July 2008
 
Hi Andy,

Thanks for the recent changes to the schema. You asked a question:
Added            <xsd:attribute name="SearchDatabase_ref" type="xsd:string"/> to DBSequence and <xsd:attribute name="accession" type="xsd:string"/> should either/both of these be set as required?

I think that the answer has to be yes. However, in the MPC_use_case_working_temp.axml file, there is: SearchDatabase_ref="", so maybe Martin could comment?


And under
  <AnalysisCollection>
    <SpectrumIdentification ... >

you made the change from
      <SpectraData_ref id="SD_1"/>
      <SearchDatabase_ref id="SDB_SwissProt"/>
to 
      <SpectraData_ref ref="SD_1"/>
      <SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>

which maybe isn't as consistent as you intended - or maybe I have missed the point?
There is also still a : 
<SpectrumIdentificationList_ref ref=...

cvList is fine, except it can only be a list of exactly 1 item at the moment... (I've not fixed the schema).

I didn't notice it last time, but the schema doesn't validate with xerces:
Need to change (in 2 places):
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?-]{1}"/>
   to
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/>
(I've not updated the schema in svn - or checked to see if xerces is correct).

Thanks,

David



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David Creasy
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