On 27 Feb 2007, at 14:25, Will Spooner wrote:
<snip>
WormMart has the same gene/transcript (CDS in WormBase's case) issues.
I solve this by 'merging' the multiple transcript values into a single
attribute in the gene_main table. See this example;
http://tinyurl.com/2x3bj5
The 'merged' attributes are pretty vital for wormbase where the 'cross
dimension multiplicity' (unconstrained dimension joins) are much more
of an issue than for Ensembl. I would like to see this approach
supported natively by BioMart/MartView, and hopefuly MartBuilder as
well.
this is what I was referring to as on of the ways of 'unifying' the
data at the higher level.
This can be done in may ways eg de-normalization on the main table
level which would
solve main->main multiplicity problem as it is in your case,
or perhaps having the dimensions with unified annotation on the higher
level
This is certainly one of the options which we are now looking for
MBuilder to support
or even screening the output dynamically as it comes out. The first two
seem to be error-free
and would perform correctly. I have some doubts about the last one but
I suppose we should
investigate all the options
a.
Will
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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
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