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

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Hi all,

I only made SearchDatabase mandatory on DBSequence, so I think this is okay?

And while you are there, could you allow multiple TranslationTable entries under DatabaseTranslationFrames?
I've added a Mascot_NA_example.xml to examples\schema_usecase_examples\working29July. 
I also think that we should change the name from DatabaseTranslationFrames to DatabaseTranslation:

Done.

I also think that we should change the name from DatabaseTranslationFrames to DatabaseTranslation

Done.

Since I've actually included the table, there is no need to reference the NCBI ontology (which doesn't exist), and this then also copes with the custom case? Can we also allow multiple cv items in the translation table so the start codons can be specified?
If anyone sees a problem, let me know otherwise I'll change the example, add details to the wiki documentation and sign off issue #24

i.e. Make the reference to CVParam 0..*? Done.

Speak at 4, cheers

Andy

From: psi...@li... [mailto:psi...@li...] On Behalf Of David Creasy
Sent: 31 July 2008 13:15
To: Martin Eisenacher
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] Changes to schema on 29th July 2008

Hi Martin, Andy

It's in schema_usecase_examples\working29July - probably added by Andy actually.
And yes, of course you are right about it being optional. (Could you add a note to the documentation as to why it's optional)

Sorry about that Andy, could you undo those changes.

And while you are there, could you allow multiple TranslationTable entries under DatabaseTranslationFrames?
I've added a Mascot_NA_example.xml to examples\schema_usecase_examples\working29July. 
I also think that we should change the name from DatabaseTranslationFrames to DatabaseTranslation:

      <DatabaseTranslationFrames frames="1,2,3,4,5,6">
        <TranslationTable id="0" name="Unspecified">
          <pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="" />
        </TranslationTable>
        <TranslationTable id="1" name="Standard">
          <pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG " />
        </TranslationTable>
        <TranslationTable id="2" name="Vertebrate Mitochondrial">
          <pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG " />
...

Since I've actually included the table, there is no need to reference the NCBI ontology (which doesn't exist), and this then also copes with the custom case? Can we also allow multiple cv items in the translation table so the start codons can be specified?
If anyone sees a problem, let me know otherwise I'll change the example, add details to the wiki documentation and sign off issue #24

Thanks,
David

Martin Eisenacher wrote: 

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

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898