Re: [Psidev-pi-dev] enzyme definition

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

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
>>> 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
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-- 
David Creasy
Matrix Science
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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