Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday 21st May at 4:00pm UK time

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

Hi Angel,

Angel Pizarro wrote:
> On Tue, May 20, 2008 at 6:14 AM, David Creasy <dc...@ma... 
> <mailto:dc...@ma...>> wrote:
> 
>     Agenda:
>     1. Review protein grouping example at:
> 
>     http://code.google.com/p/psi-pi/source/browse/trunk/examples/schema_usecase_examples/working19May/F001350.xml
> 
> 
> Several issues with this example. First listed peptides are duplicated 
> in places. Simple to edit the example to fix this.
Ah yes, thank-you. This is generated by a script, so I'll just change 
the script to not output duplicates...

However, there will be more peptides because, for the prophets and 
Scaffold, they need to see a larger number of hits (and misses!) to get 
stats.

> 
> Second the "identifier" attribute (in the FuGE sense) should be as close 
> to a GUID as possible, allowing references from other documents (or into 
> this document) using solely the identifier.  "3_1" does not do this. 
> Also there are other places in the document where the same string is 
> used to identify different object types. 
Yes, I agree and I'll change this - maybe by adding a prefix for the 
different 'types' if that sounds reasonable?

> 
> Choices are to fix this in the examples and make this clear to the 
> world, or encode this usage more forcefully within the schema.
Not sure how we'd enforce in the schema? Maybe discuss at the telecon?

(btw, Last week, we decided that meaningful names weren't important for 
the IDs)

David
> 
> -angel

-- 
David Creasy
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