Hi Jennifer,
I am pretty confident it would work. Please connect (MartEditor) to
ensembl with the credential i sent earlier on as a screen shot.
File->Import gene_ensembl
look for AttributePage link_attributes. see the settings for this page,
its group, collection and attributes inside. All have hideDisplay = true
Once you hvae these settings in your mart,
do Export on your mart and redo, perl bin/configure...... with --clean
kill/restart apache.
All should work fine..
Best,
Syed
Mead, Jennifer wrote:
Hi Syed
I have now added all fields that should be omitted from the interface into an attribute collection called 'dont_display'. I set hideDisplay for this collection to '1' and then tried 'true'. Neither work, so I now see all the fields I'd like to hide in one place on the interface :-P Anything else I can try?
If I use hidden 'true' will this be a big issue? I don't quite understand the implication for putting 'hidden'. In the documentation its says "it will be ignored by the BioMart APIs which is useful for turning off an attribute or filter that you do not want to reappear next time you update the configuration against the database" does it really affect my biomart, then?
Thanks,
Jenny
-----Original Message-----
From: Syed Haider [mailto:[email protected]]
Sent: 29 April 2009 16:41
To: Mead, Jennifer
Cc: Junjun Zhang
Subject: Re: [mart-dev] Federating queries - thanks, and hideDisplay issues
Hi Jennifer,
Unfortunately, its seems incosistent, rather broken :) Please set
hideDisplay of everthing upstream -> (AttributeCollection,
AttribtueGroup, AttributePage for that attribute), all will disappear. I
presume thats not what you want. The best is to declare an
attributePage, group, collection (hideDisplay of all these set to true)
and organise all those attributes (with hideDisplay set to true) which
you want to hide from interface under the said tree.
Best,
Syed
Mead, Jennifer wrote:
Thanks Syed and Junjun,
I will look into this for federating my queries asap, and get back to you on
how it goes. Before I get cracking though, a little thing is bugging me. When
I set hideDisplay to 'true' for my attributes, they don't disappear from my
martview interface. I have tried exporting it, running the 'blah blah --clean'
command, clicked the 'new' button and have restarted apache but nothing seems
to get rid of them. The weird thing is it works for hiding filters? Am I
going mad?
Thanks
Jenny
-----Original Message-----
From: Syed Haider [mailto:[email protected]]
Sent: 29 April 2009 15:12
To: Mead, Jennifer
Cc: [email protected]
Subject: Re: [mart-dev] Federating queries
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
