psidev-pi-dev

[Psidev-pi-dev] Ambiguous residues - CV

[David C. <dc...@ma...>]

Hi all,

We need CV for the <AmbiguousResidue> element in the analysisXML 
MassTable. This is when, for example, a search engine sees an 'X' in the 
fasta file and it tries every other defined residue mass. We decided 
that we wanted to use CV here in case a search engine implements complex 
rules for these ambiguous residues.

I propose 2 initial CV items to allow either mass or previously defined 
residue.  An example of each type shown in context below:

<MassTable is="MT1">
  <Residue Code="A" Mass="71.037114"/>
  ...
  <Residue Code="Y" Mass="163.063329"/>

  <AmbiguousResidue Code="B">
    <pf:cvParam accession="PI:xxxx" name="Alternate single letter codes" 
cvRef="PSI-PI" value="DN"/>
  </AmbiguousResidue>
  <AmbiguousResidue Code="Z">
    <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI" 
value="129.042593"/>
    <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI" 
value="128.058578"/>
  </AmbiguousResidue>
  . . .
</MassTable>

The "Alternate mass" item would be: unitAccession="UO:0000221" 
unitName="dalton".

Does this sound reasonable?

Cheers,

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

Re: [Psidev-pi-dev] Ambiguous residues - CV

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

Looks fine to me, only minor consideration might be the "value" data type for:
Alternate single letter codes. You could imagine values getting encoded as "DN"
"D N" "D,N" or "[D/N]" etc.

Elsewhere in the AnalysisXML schema, we have defined an extension data type
listOfChars, which enforces that values are given as space separated chars: "D N
M", it would be nice to follow a similar convention although I don't know if it
would make sense to put this newly defined data type into the CV?

Cheers, Andy




> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 24 November 2008 14:43
> To: psi...@li...
> Subject: [Psidev-pi-dev] Ambiguous residues - CV
> 
> Hi all,
> 
> We need CV for the <AmbiguousResidue> element in the analysisXML
> MassTable. This is when, for example, a search engine sees an 'X' in the
> fasta file and it tries every other defined residue mass. We decided
> that we wanted to use CV here in case a search engine implements complex
> rules for these ambiguous residues.
> 
> I propose 2 initial CV items to allow either mass or previously defined
> residue.  An example of each type shown in context below:
> 
> <MassTable is="MT1">
>   <Residue Code="A" Mass="71.037114"/>
>   ...
>   <Residue Code="Y" Mass="163.063329"/>
> 
>   <AmbiguousResidue Code="B">
>     <pf:cvParam accession="PI:xxxx" name="Alternate single letter codes"
> cvRef="PSI-PI" value="DN"/>
>   </AmbiguousResidue>
>   <AmbiguousResidue Code="Z">
>     <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
> value="129.042593"/>
>     <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
> value="128.058578"/>
>   </AmbiguousResidue>
>   . . .
> </MassTable>
> 
> The "Alternate mass" item would be: unitAccession="UO:0000221"
> unitName="dalton".
> 
> Does this sound reasonable?
> 
> Cheers,
> 
> 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
> 
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Re: [Psidev-pi-dev] Ambiguous residues - CV

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

Hi!

Davids proposal works well for Sequest and our MPC use case.

I agree with Andy, that we should do it analogously to e.g. the
"residues" attribute of <Modification>.

As I understood the obo type definitions correspond to xsd types;
including more complex types like "psi-pi:listOfChars" looks 
unnecessarily complex to me.


What do you think about:?
...
   <AmbiguousResidue Code="B" ResidueRef="D N"/>
   <AmbiguousResidue Code="Z">
     <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
 value="129.042593"/>
     <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
 value="128.058578"/>
   </AmbiguousResidue> 

ResidueRef can be type listOfChar.

Disadvantage is the mix of schema and CVParam mechanisms...

  Bye
    Martin


> -----Ursprüngliche Nachricht-----
> Von: Jones, Andy [mailto:And...@li...]
> Gesendet: Monday, November 24, 2008 4:07 PM
> An: psi...@li...
> Betreff: Re: [Psidev-pi-dev] Ambiguous residues - CV
> 
> Looks fine to me, only minor consideration might be the "value" data type for:
> Alternate single letter codes. You could imagine values getting encoded as "DN"
> "D N" "D,N" or "[D/N]" etc.
> 
> Elsewhere in the AnalysisXML schema, we have defined an extension data type
> listOfChars, which enforces that values are given as space separated chars: "D N
> M", it would be nice to follow a similar convention although I don't know if it
> would make sense to put this newly defined data type into the CV?
> 
> Cheers, Andy
> 
> 
> 
> 
> > -----Original Message-----
> > From: David Creasy [mailto:dc...@ma...]
> > Sent: 24 November 2008 14:43
> > To: psi...@li...
> > Subject: [Psidev-pi-dev] Ambiguous residues - CV
> >
> > Hi all,
> >
> > We need CV for the <AmbiguousResidue> element in the analysisXML
> > MassTable. This is when, for example, a search engine sees an 'X' in the
> > fasta file and it tries every other defined residue mass. We decided
> > that we wanted to use CV here in case a search engine implements complex
> > rules for these ambiguous residues.
> >
> > I propose 2 initial CV items to allow either mass or previously defined
> > residue.  An example of each type shown in context below:
> >
> > <MassTable is="MT1">
> >   <Residue Code="A" Mass="71.037114"/>
> >   ...
> >   <Residue Code="Y" Mass="163.063329"/>
> >
> >   <AmbiguousResidue Code="B">
> >     <pf:cvParam accession="PI:xxxx" name="Alternate single letter codes"
> > cvRef="PSI-PI" value="DN"/>
> >   </AmbiguousResidue>
> >   <AmbiguousResidue Code="Z">
> >     <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
> > value="129.042593"/>
> >     <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI"
> > value="128.058578"/>
> >   </AmbiguousResidue>
> >   . . .
> > </MassTable>
> >
> > The "Alternate mass" item would be: unitAccession="UO:0000221"
> > unitName="dalton".
> >
> > Does this sound reasonable?
> >
> > Cheers,
> >
> > 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
> >
> >
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> > Build the coolest Linux based applications with Moblin SDK & win great prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________
> > Psidev-pi-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev