On 7 Jul 2006, at 18:36, Ronaldo Raposo wrote:
Hello Damian,
Thank you for the responses. In fact, we just expect to do two
things: the first, and the most important, is to link one database
that I created in my local computer to other database created locally
too or other database I downloaded from biomart site. How can we link
them?
you need to create an exportable in one dataset and a matching
importable
in the other. You can also use MartEditor (part of the martj package)
to access any of the public BioMart
database to see how those exportables and importables look like in
public datasets.
(Connection details below)
The second is my created database link with a database that is in
biomart site.
We have to use a web-service technology to link them?
you can if you prefer. The BioMart server will do it for you. You just
need
to specify if you want to use web service. There are two ways of
accessing BioMart
databases either through a web service or directly talking to the
public database server.
In order to specify the connection details you need to edit
defaultMartRegistry.xml
file which comes with the software. You can either go for
RegistryURLPointer (web service)
or RegistryDBPointer (direct RDBMS).
If you have matching importables in any of your datasets your local
BioMart server
will automatically create appropriate links.
BTW, not all databases that are available from the central server are
located
on the BioMart site. Central server just provides a reference point so
you can find them.
To give you an idea below is a registry file which identifies the
databases:
web service:
http://www.biomart.org/biomart/martservice?type=registry
direct RDBMS:
?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="dicty" visible="0">
<MartURLLocation path="" host="www.dictybase.org" name="dicty"
serverVirtualSchema="dictyMart" displayName="DICTYBASE (NORTHWESTERN)"
port="80" visible="1" default="1" martUser="" includeDatasets=""
redirect="1" />
</virtualSchema>
<virtualSchema name="default" visible="0">
<MartDBLocation databaseType="mysql" host="ensembldb.ensembl.org"
database="ensembl_mart_39" name="ensembl" displayName="ENSEMBL 39
(SANGER)" port="3306" schema="ensembl_mart_39" user="anonymous"
password="" visible="1" default="1" martUser="" includeDatasets=""
/><MartDBLocation databaseType="mysql" host="ensembldb.ensembl.org"
database="sequence_mart_39" name="sequence" displayName="SEQUENCE 39
(SANGER)" port="3306" schema="sequence_mart_39" user="anonymous"
password="" visible="0" default="0" martUser="" includeDatasets=""
/><MartDBLocation databaseType="mysql" host="ensembldb.ensembl.org"
database="snp_mart_39" name="snp" displayName="SNP 39 (SANGER)"
port="3306" schema="snp_mart_39" user="anonymous" password=""
visible="1" default="0" martUser="" includeDatasets=""
/><MartDBLocation databaseType="mysql" host="ensembldb.ensembl.org"
database="vega_mart_39" name="vega" displayName="VEGA 39 (SANGER)"
port="3306" schema="vega_mart_39" user="anonymous" password=""
visible="1" default="0" martUser="" includeDatasets=""
/><MartDBLocation databaseType="mysql" host="martdb.ebi.ac.uk"
database="uniprot_mart_17" name="uniprot" displayName="UNIPROT
PROTOTYPE 4-5 (EBI)" port="3306" schema="uniprot_mart_17"
user="anonymous" password="" visible="1" default="0" martUser=""
includeDatasets="" /><MartDBLocation databaseType="mysql"
host="martdb.ebi.ac.uk" database="msd_mart_4" name="msd"
displayName="MSD PROTOTYPE 4 (EBI)" port="3306" schema="msd_mart_4"
user="anonymous" password="" visible="1" default="0" martUser=""
includeDatasets="" /><MartDBLocation databaseType="mysql"
host="aceserver.cshl.org" database="wormmart_current" name="wormbase"
displayName="WORMBASE CURRENT (CSHL)" port="3306"
schema="wormmart_current" user="anonymous" password="" visible="1"
default="0" martUser="" includeDatasets="" />
</virtualSchema>
</MartRegistry>
And if I do a query in martview website and receive a output file, how
will we use the file to be the filter of our local database?
Thanks once more for the gentility to answer our many doubts.
Best Regards,
Ronaldo Raposo.
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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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