Hi Jennifer,
----------
MARTEDITOR
----------
you need to declare importable/exportable pairs (see docs for details).
Exportable is an attribute which one dataset returns to the linkable
dataset having an importable (which is a filter) having *same* name.
please connect to ensembl using the credentials and see possible
exportables/importables you can use to link up.
to connect, you need credentials shown here:
http://www.ebi.ac.uk/~syed/MartEditor_ensembl.png
---------
MartView
---------
to make ensembl available as second dataset, you need to add it to your
registry file and then reconfigure (perl bin/configure.pl.....) and
restart apache.
you need to add the following to your registry for ensembl:
<MartURLLocation database="ensembl_mart_53" default="1"
displayName="ENSEMBL 53 GENES (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="ensembl"
path="/biomart/martservice" port="80" serverVirtualSchema="default"
visible="1" />
<MartURLLocation database="genomic_features_mart_53" default="0"
displayName="ENSEMBL 53 GENOMIC FEATURES (SANGER UK)"
host="www.biomart.org" includeDatasets="" martUser=""
name="genomic_features" path="/biomart/martservice" port="80"
serverVirtualSchema="default" visible="0" />
<MartURLLocation database="ontology_mart_53" default="0"
displayName="ENSEMBL 53 ONTOLOGY (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="ontology"
path="/biomart/martservice" port="80" serverVirtualSchema="default"
visible="0" />
<MartURLLocation database="sequence_mart_53" default="0"
displayName="ENSEMBL 53 SEQUENCE (SANGER UK)" host="www.biomart.org"
includeDatasets="" martUser="" name="sequence"
path="/biomart/martservice" port="80" serverVirtualSchema="default"
visible="0" />
Hope this helps,
Syed
Mead, Jennifer wrote:
Hi guys,
I would like to perform queries using Martview for my own mart AND
Ensembl database(s) at the same time. Basically, in my mart DB I have
stored Ensembl gene ids for each entry, but I have not stored the
protein names/descriptions. Instead I was hoping to perform federated
queries, whereby I could use the Ensembl gene id in my mart to link to
Ensembl at EBI to retrieve the descriptions on the fly. This way I hope
to keep my database protein info up-to-date and save space in my local
mart. Where can I find information regarding the implementation of
federated queries using martbuilder/marteditor/martview? Would it
perhaps be possible for a live example of this to be put on the FAQs
page at www.biomart.org <http://www.biomart.org>? One little
complication is that my gene ids are not just human – but they are all
from species for which Ensembl has an existing build.
Thanks very much,
Jenny
