[Gusdev-rad-issues] Re: [Gusdev-gusdev] prerequisites for RAD ArrayLoader

[Elisabetta M. <man...@pc...>]

Kevin,
yes you'll need to have the relevant entry in SRes.ExternalDatabaseRelease 
if you want to enter (external_database_release_id, source_id) in any 
given GUS table and you create this in the order you outline.
For the specific case of the ArrayLoader, this pair of fields is present 
both in RAD3.Array and in views of RAD3.ElementImp and 
RAD3.CompositeElementImp.
An example of an external_database for a RAD3.Array entry might be 
ArrayExpress, if you want to indicate an identifier (through source_id) 
for the same array in another database. In our instance of RAD our arrays 
are typically pointed to an ArrayExpress array (if they are also in there) 
or to nothing, but of course you can point to anything you like.
In views of ElementImp and CompositeElementImp the external database is 
typically important as it enables to identify what the element or 
composite element on the array represent. Examples of databases that are 
of relevance here might be GenBank, IMAGE, etc. For the same array 
different elements (composite elements) on that array might point to 
different databases. For examples, for some of the non-commercial arrays 
stored in our instance of RAD, some of the spots on that array are 
identified through an image clone id, others through a GenBank, etc. 
depending on available information.
The source_id always refer to the main identifier in the db pointed to by 
external database id, which identifies the specific entry. For example it 
would be the accession_num for GenBank, the image clone_id for IMAGE, etc. 
Elisabetta
P.S. When you send emails to the GUS list that are of particular 
interest to RAD, could you please also cc the rad-issues source forge 
list, here copied? If you have not subscribed to the latter, I recommend 
you do.

---

On Mon, 15 Nov 2004, Kevin Murphy wrote:

> When loading a new array using GUS/RAD/Plugin/ArrayLoader.pm, what are the 
> database prerequisites for the external_database_release_id and source_id 
> columns in the input data file?
>
> Are you supposed to create an SRES.ExternalDatabase record with, e.g. a 
> 'name' column value of 'FooArray123', then create a corresponding 
> SRES.ExternalDatabaseRelease record, and use that 
> external_database_release_id in the data file?
>
> And what of the source_id column?
>
> Thanks,
> Kevin Murphy
>
>
>
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