On 27 Nov 2006, at 15:07, Roloff, Tim wrote:
Hey there,
I ran into a couple of problems/questions while trying to set up a
Biomart database.
- When we put a RegistryDBPointer and a MartDBLocation in the
defaultMartRegistry.xml, only the the RegistryDBPointer is used for the
database location and we do not see our local test databases. They do
however show up, if we only use MartDBLocations in the .xml. Is that
supposed to be that way or could both be loaded?
this is a bug in 0.4, if you want to both of them be loaded please
replace RegistryDBPointer with MartDBLocations it contains
and it should work fine
- We were trying to use Importables/Exportables to combine our datasets
with the ENSEMBL or Uniprot datasets. We had however difficulties to
figure out the exact naming of the corresponding values in
ENSEMBL/Uniprot. Is there a list of all Exportables/importables
somewhere, that one could use to do the matching?
yes, you can use MartEditor (part of martj) to open appropriate dataset
configs
on ensembldb.ensembl.org and martdb.ebi.ac.uk
- Would it be possible to use more than two datasets for one query in
Biomart?
yes, in 0.4 you can only combine filters from two datasets and
attributes from one
but in coming 0.5 you will be combine both
- Some of the biomart datasets on the web are already version 0.5 and
hence not compatible with the current release.
could you give us more details? not sure if I understand
Does anyone know, when v
0.5 will be available?
the release is imminent :)
a.
I hope these are not to many stupid questions and would greatly
appreciate any help.
Tim
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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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