Dear Julie,
[email protected] wrote:
Hi,
I'm terribly sorry for the delay of my answer but I had to finish
another project first.
I did get your tutorial but I still can't manage having the automatic
printing of two different datasets, in the left hand side of martview.
I've followed the tutorial for the definition of Exportables and
Importables p10.
I still have no results on this work ! I've saved the two last
configurations with marteditor as you told me so you can have a look
at it. (joinEssai2.zip is last one I've made)
For the moment, I'm gessing that I do not understand which table
fields and table keys are needed when reading gene_id and gene_id_key
on the tutorial. Therefore I might not have worked with the correct
corresponding names.
In a filter or an attribute (used respectively for the importable on one
side and exportable on the other side), you need to specify:
- field as the column in your table
- key as the name of the column that acts as PK in the table (can be the
same as field)
- table as the name of the table
Also, you must know that I'm trying the work on two datasets having
one field in common. However, those datasets are in the same database
whereas the exemple is made with one dataset in each database. May
this be the problem ?
It does not matter that they are in the same database
If not, can I get the translation of the names used in the tutorial with:
- tb1.key and tb2.key meaning the primary key of each tables.
- tb1.field and tb2.field meaning the common field between the two
tables. (I know that their names may be different as the naming is
automaticly modified when creating a dataset.)
In the case of the tutorial, you have an exportable called
"export_gene_id" created on the attribute called "gene_id" and whose
properties are: field=gene_id_key, key=gene_id_key &
tableConstraint=main. In other words, gene_id_key is both the PK of the
main table and the column of interest
You also have an importable called "import_gene_id" created on the
filter called "gene_id" (could have been different than the exportable
here) and whose properties are: field=gene_id, key=pathway_id_key &
tableConstraint=gene_dm. In other words, this time pathway_id_key is the
PK of table gene__dm but it's on the column gene_id that we filter, and
it's on this column that the importable will apply (yet you still need
to specify the key of the table)
Finally, in both the importable & the exportable, you have
linkName=name=link_gene_id which tells the system to link these 2 together.
My other question will be: Is the automatic printing of the 'double
left hand menu' automatic once I've defined the exportables and the
importables between two datasets or do I have to interfere in
biomart-perl to make my result printable?
You do not need to do anything but rerun configure.pl + restart apache.
What will happen is that you will see your 2 datasets in the list. When
you'll chose the one that has the importable, then you'll see a second
one appear on the left-hand side. The converse is not true (the
exportable side will not show a 2nd dataset).
Please let me know if you need any explanation in what I have done.
Thanks again for your patience and your help.
Hope that helps!! :)
Regards,
Anthony
Julie
*Anthony Cros <[email protected]>*
Envoyé par : [email protected]
25/06/2009 20:53
A
"[email protected]" <[email protected]>,
"[email protected]" <[email protected]>
cc
Objet
Re: [mart-dev] Printing multiple dataset in left hand menu
Hi Julie,
Before we go deeper into your problem, it appears you didn't specify the
linkName and the name of your importable and exportable (linkName=name
and they have to be the same for both the importable and the
exportable). You must also specify a list of filters in the importable
and a list of attribute in the exportable (that's what the join is going
to happen on). Can you please try to add these and let me know how it
goes?
I'm going to see if we can send you the tutorial quickly too.
Thanks and have a great day,
Anthony
PS: if you have problems with English, I can definitely assist you in
French (the only thing is that I'll probably have to translate
everything so everyone can follow)
[email protected] wrote:
>
> Hi,
>
> I've read the 5.1.2.5 paragraph in the documentation to create my
> exportables and importables between my datasets called A_THALIANA and
> GENE_ONTOLOGY.
> Here are my XML configuration files that I've managed to create with
> marteditor.
>
>
>
> I have no access to the tutorial of Biomart.
>
> I'm terribly sorry but my english must not be that good. I have
> managed to create multiple marts, datasets and attributes but I can't
> manage to arrange my Biomart Server to get the following structure:
>
>
>
> Can you explain to me the all procedure that I need to do to get such
> a view.
> Also, I don't understand how is my importables/exportables
> configuration taken into account by martview?
>
> Thanks for your help,
>
> Julie
>
>
> ------------------------------------------------------
> >
> Hi Julie,
>
> No you definitely don't need to have 2 different marts to do this. If
> you have too much trouble configuring your datasets, you can send us
> your XML configuration files (File-> Save All => creates several XMLs
> file) so we can have a look at it.
> Have a good day,
>
> Anthony
>
> PS: you cannot attache anything to an email on mart-dev so you would
> need to send the attachment in private
>
>
> [email protected] wrote:
> >
> > Hi,
> >
> > I've created my linking datasets but with only one mart.
> > The left hand side menu of my BioMart server is still the same. Is the
> > fact of having multiple marts is obligatory?
> >
> > Thanks again for your answers.
> >
> > Julie
> --------------------------------------------------------
> >Sure,
>
> >Hi Julie, you can find some info on how to do this in the
documentation,
> >p51, the paragraph starting with "Datasets can be linked together...".
> >The tutorial provides more details (p11 onwards).
> >Let us know if you need more help!
> >Cheers,
>
> >Anthony
>
> >Arek Kasprzyk wrote:
> >
> > On 18/06/09 11:26 AM, "[email protected]"
> <[email protected]>
> > wrote:
> >
> >
> >> Thanks !
> >>
> >> You have perfectly understood what I wanted to do.
> >> The problem is that I do not know how to make sure that my datasets
> connect to
> >> importables and exportables.
> >> Is there a specific part on that in the documentation?
> >>
> >
> >
> > Sure, guys - could you point Julie to where to find info on
> > exportables/importables please? I am pretty sure there is some info
> about it
> > in our documentation under MEditor section. Maybe our tutorial would
> help as
> > well?
> >
> >
> > Cheers,
> > A.
> >
> >
> >
> >
> >> Julie
--
*Anthony Cros
*Database/Application Programmer
*Ontario Institute for Cancer Research
*MaRS Centre, South Tower
101 College Street, Suite 600
Toronto, Ontario, Canada M5G 0A3
Tel: 647-260-7974
Toll-free: 1-866-678-6427
www.oicr.on.ca
This message and any attachments may contain confidential and/or
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originally intended is strictly prohibited. If you have received this
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--
*Anthony Cros
*Database/Application Programmer
*Ontario Institute for Cancer Research
*MaRS Centre, South Tower
101 College Street, Suite 600
Toronto, Ontario, Canada M5G 0A3
Tel: 647-260-7974
Toll-free: 1-866-678-6427
www.oicr.on.ca
This message and any attachments may contain confidential and/or
privileged information for the sole use of the intended recipient. Any
review or distribution by anyone other than the person for whom it was
originally intended is strictly prohibited. If you have received this
message in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this message may
not be that of the organization.
