Apologies if I'm missing something very obvious, but I'm struggling to figure out how to make BioMart behave the way I want.
What I've been asked to do is to use the BioMart framework to produce a portal that lab members can use to access results from the different experiments that have been done in our lab. So the idea is that the user can go to the BioMart page, input <gene name> and get back something like a page displaying data from any experiment associated with that gene name.
Whilst I can follow the instructions in the BioMart docs to configure one dataset, I can't work out how to add multiple datasets to my mart.
If I create multiple configs, when I start the server I get a page with links to each config name. Clicking on one of those takes me to a query page with the headings "Database" and "Dataset". "Database" == the name of my config. "Dataset" == the name of my dataset (phew!).
This isn't entirely what I expected, which makes me worried that I'm fundamentally misunderstanding something - I can I add multiple datasets to one config? What I want to achieve is something like the main BioMart's MartView - drop down menus for the user to select a database and datasets from.
I would then like to present data to the user as a report with the gene name as the key and results from the different data sources (in this case experiment types) as different sections of the report.
Jane Charlesworth PhD
Wellcome Trust Centre for Cell Biology,
Institute of Cell Biology,
School of Biological Sciences,
The University of Edinburgh,
6.33 Swann Building
Edinburgh EH9 3JR
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In regard to the report, is this something close to what you'd like to do? https://dcc.icgc.org/martreport/?report=report&mart=gene_report&ensembl_gene_id=ENSG00000133703
From what you described, BioMart definitely can be used to manage data from different experiments and make them interactively searchable. To get yourself familiar with BioMart and how organizes data etc, you may want to take a look at http://dcc.icgc.org, here there are all different types of experiments data, and many of them are linked to genes. If you are interested in figuring out how things work under the hood, you can even set up a mirror of that Data Portal on your own machine without much effort. All you need to do is to checkout BioMart 0.8 rc6 release, and open the registry file: icgc6.xml using MartConfigurator and deploy it.
Please feel free to let us know if you have any specific questions.
From: Jane Charlesworth <[hidden email]>
Date: Thu, 25 Aug 2011 10:58:37 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] Adding multiple datasets
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