Hi,
We at VectorBase are basically in a position where we'll be hosting
several organisms based on data coming out of the Ensembl pipeline.
Currently, that means A. gambiae and A. aegypti. We actually transform
the data into the Chado schema (using the Ensembl Perl API) and then add
some additional data. Once all the data is integrated, we export for use
with Mart. The reason that I've been exploring partitioning is because
creating identical datasets seems like doing it the long way round, but
if partitioning doesn't work yet...
Is there at least a way to fetch, modify, and then re-upload the Mart
schemas in XML format to allow easier search-and-replace of organism
names? It seems that the Open and Save menu items are missing from the
0.5 MEditor.
--E.O. Stinson
Arek Kasprzyk wrote:
On 5 Mar 2007, at 22:19, E.O. Stinson wrote:
Hi all,
I've been trying to get dataset partitioning working and it seems to
be broken in the release of MartEditor that's publicly available. (For
instance, there is no way to add partitions, although I've modified
the code I have to get around that.) Now I'm realizing that it's not
actually creating the dataset partitions in the database. Instead,
it's creating a single dataset with the name of the template, rather
than several based on the partition names. Is there a trick to this
I'm missing, or a version of MartEditor that does this better? Should
I be trying MartBuilder instead? Alternatively, is the other way to do
this to create separate datasets for every organism? If so, is there a
way to save and load individual XML files? Those seem to have
disappeared since version 0.4.
For reference, I'm using the release-0_5 CVS branch of MartEditor.
Hi,
I am afraid partitioning is not yet properly supported. This feature
will require changes to MBuilder and substantial changes
to the future releases of MEditor. However, could you give us more
details on what you are trying to achieve? It is likely
that we can find the way round it as we of course are in the same
position and need to add ensembl species quite often.
Are you working with existing XML? eg ensembl? if yes, what version of
Ensembl is that?
Are you simply trying to add new species? or you want to do something
more complicated?
if so, could you give us more details?
thanks,
a.
a.
Thanks,
E.O. Stinson
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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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