Re: [Mged-mage] [Mged-mage2] MAGETAB spec comments

[Tim R. <ra...@eb...>]

Hi,

Sorry to disturb the list further with my ramblings. Having just hit the 
send button it occurred to me that a more consistent way to do this might 
be to allow Protocol REF and Array Design REF to be associated with Term 
Source REF columns. It's more flexible and only a minor addition to the 
specification.

Cheers,

Tim

-- 
Tim Rayner
ArrayExpress

On Thu, 18 Jan 2007, Tim Rayner wrote:

> Hi,
>
> One possible alteration which has come up is a means of indicating a
> source database for protocol or array design accessions, where such
> information is reused between experiments. I'd like to propose that we
> allow the Protocol REF and Array Design REF columns to refer to the IDF
> Term Source Name using either square brackets or parentheses, e.g.:
>
> Protocol REF [ArrayExpress]
>
> Array Design REF [GEO]
>
> where ArrayExpress or GEO are explicitly listed in the IDF as Term
> Sources. I'd also suggest that in the absence of such tags it is assumed
> that the identifier is local to the context in which the SDRF is used,
> e.g. assuming ArrayExpress accessions for submissions to ArrayExpress.
>
> Note that there is scope for using the Protocol REF:namespace syntax to
> add an external namespace to identifiers in the SDRF, but that doesn't
> really work for accessions which don't have namespaces (for good or ill).
>
> Any comments?
>
> Cheers,
>
> Tim
>
>