Hi,
While we're talking about the results section. I've wondered if a "unique
records only" option could be provided - to the average biologist user, the
following query brings back duplicated genes (because the PFAM domains are
features of transcripts, which I have deselected from the output attributes).
<Query virtualSchemaName = "default" Header = "1" count = "" softwareVersion =
"0.5" >
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Attribute name = "ensembl_gene_id" />
<Filter name = "pfam" value = "PF00169"/>
</Dataset>
</Query>
However, we can leave the default gene + transcript attributes and instead
provide two PFAM ids (that I know are sometimes in the same protein). Then
the results again contain some duplicate records (although adding the PFAM id
output attribute would fix this of course).
<Query virtualSchemaName = "default" Header = "1" count = "" softwareVersion =
"0.5" >
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Attribute name = "ensembl_gene_id" />
<Attribute name = "ensembl_transcript_id" />
<Filter name = "pfam" value = "PF00169,PF00017"/>
</Dataset>
</Query>
snippet:
ENSG00000102010 ENST00000342014
ENSG00000102010 ENST00000342014
ENSG00000102010 ENST00000348343
ENSG00000102010 ENST00000348343
ENSG00000102010 ENST00000357607
ENSG00000102010 ENST00000357607
ENSG00000102010 ENST00000380391
ENSG00000102010 ENST00000380391
I note that the gene count ("count" button) is always correct however.
What do people think?
cheers,
Bob.
Arek Kasprzyk writes:
>
> On 26 Jan 2007, at 14:43, David Croft wrote:
>
> > Hi Arek,
> >
> >> Sounds like a good suggestion, we can consider that. At the moment
> >> you can only ask for first 10, 20, 50 .... 200 or the whole lot but
> >> not
> >> the pagination that (I think) you have in mind
> >
> > Yes, that's right - similar to what you get when you go to Google.
> > It would be kind of cool if the page displayed the total count of
> > results and told you that you are on page 3 of 28 (or whatever)
> > and gave you buttons to go back a page or forward a page.
> >
>
> not sure about this :) we could certainly add 'next' 'back' or
> equivalents
> but the total count and would be a bit more problematic. We do not have
> all the results during preview yet and the total count tend to be often
> expensive so we do not do it as default. Let us try to think about at
> least
> some of it
>
> a.
>
>
> > Cheers,
> >
> > David.
> >
> >
>
>
> ------------------------------------------------------------------------
> -------
> Arek Kasprzyk
> EMBL-European Bioinformatics Institute.
> Wellcome Trust Genome Campus, Hinxton,
> Cambridge CB10 1SD, UK.
> Tel: +44-(0)1223-494606
> Fax: +44-(0)1223-494468
> ------------------------------------------------------------------------
> -------
>
>
>
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
