On 12 Jan 2007, at 17:15, Marina Olhovsky wrote:
I guess the real question now becomes: How do I set
exportables/importables correctly? I found a paragraph on that on
page 29 and 31 of the manual, but, unfortunately, I didn't find any
details. Where would I find this sort of info? Thanks so much.
ok, the principle is very simple, the importable is an ordered list of
filters and
an exportable is an ordered list of attributes. The software will join
them
if they live on the separate datasets but have the same name.
In practice they are usually a single element lists and this boils down
then to mapping two datasets based on a common identifier.
In this simple scenario, what you have to do is the following:
Identify a common identifier in dataset A and dataset B
let's say ensembl_id
now in dataset A, you make sure that there is an attribute mapped
to a column containing ensembl_id. Let's call this attribute
"ensembl_attribute".
In this dataset you need to create an exportable and put in the
attributes field
"ensembl_attribute". Let's call this exportable "ENSEMBLID"
now, in dataset B you need to make sure that there is a filter pointing
to the column containing ensembl_id, let's call this filter
"ensembl_filter".
You need now to create an importable and put "ensembl_filter" in the
filter list.
In order for this to work you need to call this importable also
"ENSEMBLID"
Now all you have to do is to start up a software making sure that the
registry
file points to the mart(s) where dataset A and B live and the software
will automatically
create links on the startup
In case you are wondring, MEditor has a right click function "create
exportable",
the same for importable
hope that helps,
a.
Marina.
-----Original Message-----
From: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Sent: Thu 1/11/2007 3:29 PM
To: Marina Olhovsky
Cc: mart-dev ((E-mail))
Subject: Re: URL registry config
On 11 Jan 2007, at 19:31, Marina Olhovsky wrote:
> Hi Arek,
>
> So sorry for the confusion! I was actually trying to do 2 things
> here: 1) see if I could simultaneously search my local dataset and
> Ensembl (some reagents in my dataset have their Ensembl ID stored
as a
> property),
yes you can do it: you need
MartURLLocation to www.biomart.org
MartDBLocation to your database
(you also need to have importables set correctly on your datasets)
> and 2) link 2 datasets in my own mart on localhost. Think I
confused
> too many things............
>
for that you just need
MartDBLocation to your own mart plus
exportables and importables set correctly on your datastes.
a.
> Best regards,
> Marina.
>
>
>
---------------------------------------------------------------------
> Marina -
>
> this URLLocation will only pick up one dataset called "my_dataset".
> (if there is no such dataset on web server localhost:5555 then you
> will
> see the error message as above)
> The server you are trying to configure will talk to another
> local BioMart server running on port 5555 using a web service.
> If you want more than one dataset you need to leave
'includeDatasets'
> empty.
>
>
> However, I am not sure that I understand why you want to talk to
> another local BioMart server
> rather than talking directly to your postgress instance through
> MartDBLocation?
> Is it not the case that you need MartDBLocation set to talk to your
> postgress database or
> MartURLLocation talking to a public server eg. www.biomart.org?
Why
> are
> you trying
> to 'chain' local servers like that? I simply don't understand what
> you
> are trying to do. Could
> you elaborate on this a bit? maybe there is an alternative way of
> doing
> what you are trying to do
>
>
> a.
>
---------------------------------------------------------------------
>
>
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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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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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