Uniprot parser and the protein table

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Uniprot parser and the protein table

James Blackshaw
Hi,

While first starting to upgrade Intermine late last year, I changed the
database schema slightly as my parser for UniProt was unable to create a
newattribute in Protein and assign a value to it. My Gene Ontology
parser assigns a "flag" attribute in a new table galled goFlags to TRUE
to indicate if there's evidence in the GO source for a protein being
mitochondrial.

I recall being told at the workshop that parsers cannot directly
populate Protein any more. Am I right in this, or have I confused
myself, and I had to set flags this way for another reason?

-James

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Uniprot parser and the protein table

Julie Sullivan
Hi James,

The UniProt converter creates and stores Protein objects.  You should be able to
create new attributes to Protein and assign the appropriate values.

So I don't know why the flags are set up that way.  Are they used for anything
else?  Do you want to try to edit the uniprot parser again?  I'll help.

Cheers,
Julie

On 06/29/2011 05:12 PM, James Blackshaw wrote:

> Hi,
>
> While first starting to upgrade Intermine late last year, I changed the database
> schema slightly as my parser for UniProt was unable to create a newattribute in
> Protein and assign a value to it. My Gene Ontology parser assigns a "flag"
> attribute in a new table galled goFlags to TRUE to indicate if there's evidence
> in the GO source for a protein being mitochondrial.
>
> I recall being told at the workshop that parsers cannot directly populate
> Protein any more. Am I right in this, or have I confused myself, and I had to
> set flags this way for another reason?
>
> -James
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev