Re: [Psidev-pi-dev] enzyme definition

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Agreed - the two separate use cases are much clearer and can be supported.
Cheers, Andy

> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 10 October 2008 17:06
> To: Jones, Andy
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] enzyme definition
> 
> Hi all,
> 
> Yes, the use case really isn't very clear (my fault) - and looking back
> through some notes I think we are reading much more into this than is
> required. It also looks as though I've 'mangled together' two separate
> use cases that should be 1. I propose 2 different uses cases:
> 
> 1. A PMF search and an MS-MS search of the same sample can be saved in
> the same instance document as long as the result is one combined protein
> list.
> 
> 2. It should be possible to combine the results from multiple search
> engines into one AnalysisXML document. For example, the peptide
> identification results from two different search engines could be
> combined using a third tool to give one set of protein results.
> 
> 
> We don't have an example for #1 (but it's easy to produce one)
> The MPC_example.axml is an example of the second case, and I can think
> of at least one other tool that will want to produce something similar...
> 
> I don't think that this would be moving the goal posts... any comments?
> 
> http://psidev.info/index.php?q=node/371
> 
> David
> 
> 
> Jones, Andy wrote:
> > Hi all,
> >
> > I'm not sure we have completely solved this one:
> >
> > use case 3:
> >
> > "It should be possible to add the results of new searches to an existing instance
> document. For example, a PMF search and an MS-MS search of the same sample
> could be saved in the same instance document"
> >
> > In reality this use case is only be supported if there is one ProteinDetection
> event producing one ProteinDetectionList i.e. protein detection was done taking
> evidence from both PMF and MS/MS.
> >
> > I don't think we can really support it if we are implying that new proteins were
> detected in a separate process then added to the same ProteinDetectionList for
> two reasons:
> > 1) It would be pretty difficult to sort out which proteins came from which process
> when looking at the results
> > 2) The entire list can have CVParams e.g. giving stats about the process such as
> numSequences or such like, these wouldn't make sense if the list contained
> results from more than one process.
> >
> > We should clarify the use case that we only supporting the more specific use
> case above, or we need to change the schema to allow more than one
> ProteinDetectionList (which we previously voted against to avoid the problem of
> "what are the intermediate/final results").
> >
> > Cheers
> > Andy
> >
> >
> >
> >
> >
> >
> >> -----Original Message-----
> >> From: Martin Eisenacher [mailto:mar...@ru...]
> >> Sent: 09 October 2008 17:31
> >> To: 'David Creasy'; psi...@li...
> >> Subject: Re: [Psidev-pi-dev] enzyme definition
> >>
> >> Dear PSI-PI workers,
> >>
> >> I committed minor schema changes (as agreed in TeleCon 9th of October):
> >>
> >> 1) changed cardinality of <cvParam> child of <Enzyme> to: one to many (to
> allow
> >> synonyms)
> >>
> >> 2) restricted CTermGain and NTermGain to "[A-Za-z0-9 ] (basic letters of a
> >> chemical formula) (can be refined later)
> >>
> >>   Bye
> >>    Martin
> >>
> >>> -----Ursprüngliche Nachricht-----
> >>> Von: David Creasy [mailto:dc...@ma...]
> >>> Gesendet: Wednesday, October 08, 2008 7:02 PM
> >>> An: psi...@li...
> >>> Betreff: Re: [Psidev-pi-dev] enzyme definition
> >>>
> >>> Hi Martin,
> >>>
> >>> No, they've not been added to the CV yet. There are still a couple of
> >>> unresolved issues at:
> >>>
> >>> http://code.google.com/p/psi-pi/issues/detail?id=30#c30
> >>>
> >>> Any comments welcome, and then we can add to the CV and sign off this
> issue.
> >>>
> >>> David
> >>>
> >>> Martin Eisenacher wrote:
> >>>> Hi Angel, hi David,
> >>>>
> >>>> I've seen some progress on the CV terms for common enzymes
> >>>> including some OBO lines from Angel in the issue list.
> >>>>
> >>>> But the svn obo file seems to be unchanged.
> >>>> Or have you changed the location?
> >>>>
> >>>> Would be great to use it in some examples...
> >>>>
> >>>>  Bye
> >>>>    Martin
> >>>>
> >>>>
> >>> --
> >>> David Creasy
> >>> Matrix Science
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> >>>
> >>> dc...@ma...
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> --
> 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