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| − | {| class="tutorialheader"
| + | #REDIRECT [[BioMart Tutorial]] |
| − | | align="right" | {{#icon: Biomart250.png|BioMart|200|BioMart}}<br /><br />{{#icon: 170px-October2011Logo.png|October 2011 - Toronto||2009 GMOD Summer School - Toronto, Canada}}
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| − | | {{TutorialTitleLine|[[BioMart]]}}<br />
| + | |
| − | [http://gmod.org/wiki/October_2011_GMOD_Meeting 2011 GMOD Community Meeting] & <br />[http://oicr.on.ca/ Ontario Institute for Cancer Research]<br />Toronto, Canada<br />
| + | |
| − | 14 October 2011<br />
| + | |
| − | [[User:Junjun%20Zhang|Junjun Zhang]], [[User:Elena%20Rivkin|Elena Rivkin]] and [[User:Anthony%20Cros|Anthony Cros]]
| + | |
| − | |}
| + | |
| − | __NOTITLE__
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| − | | + | |
| − | | + | |
| − | This [[:Category:Tutorials|tutorial]] walks you through how to install and configure a local installation of [[BioMart]].
| + | |
| − | | + | |
| − | | + | |
| − | __TOC__
| + | |
| − | | + | |
| − | | + | |
| − | = System overview and installation =
| + | |
| − | Prerequisites for BioMart:
| + | |
| − | # Software: Java 1.6, Ant and SVN client
| + | |
| − | # OS: Linux, Mac & Windows
| + | |
| − | # Server: min. 1 GB memory, 3 GB for better performance
| + | |
| − | | + | |
| − | = Add a section here for installing VirtualBox or VMware and start up the VM =
| + | |
| − | | + | |
| − | # where to download virtualbox etc.
| + | |
| − | # where to get VM image (download? or get it from USB key)
| + | |
| − | | + | |
| − | = Downloading & Installing BioMart =
| + | |
| − | | + | |
| − | Two components are necessary for this tutorial: MartBuilder is installed form an older version of BioMart (0.7), and MartConfigurator is installed from the most recent version (0.8) (until all features are fully ported to the new version)
| + | |
| − | | + | |
| − | Installation of MartBuilder and MartConfigurator has already been done on the VM image under ~/biomart_0_7.template and ~/biomart_0_8.template, but we are going to do once together for demonstration purposes.
| + | |
| − | | + | |
| − | Refer to [http://www.biomart.org/rc6_documentation.pdf BioMart Documentation] for more information.
| + | |
| − | | + | |
| − | == Biomart 0.7 (MartJ -> MartBuilder + MartRunner) ==
| + | |
| − | | + | |
| − | MartJ contains applications necessary to create a Mart: MarBuilder and MartRunner.
| + | |
| − | | + | |
| − | Check Section 2 in [http://www.biomart.org/user-docs.pdf Installing BioMart] for more information.
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| − | | + | |
| − | Download & extract tarball content with:
| + | |
| − | | + | |
| − | $ mkdir ~/biomart_0_7 # arbitrary name of course
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| − | $ cd ~/biomart_0_7
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| − | $ wget <nowiki>ftp://anonymous@ftp.ebi.ac.uk/pub/software/biomart/martj_current/martj-bin.tgz</nowiki> # or get it from [ftp://anonymous@ftp.ebi.ac.uk/pub/software/biomart/martj_current/martj-bin.tgz MartJ]
| + | |
| − | $ tar zxvf martj-bin.tgz # creates "martj" directory
| + | |
| − | $ cd martj
| + | |
| − | $ ls bin/martbuilder.sh bin/martrunner.sh # what we care about
| + | |
| − | | + | |
| − | == Biomart 0.8 (MartConfigurator) ==
| + | |
| − | | + | |
| − | Checkout latest release using SVN:
| + | |
| − | | + | |
| − | $ mkdir ~/biomart_0_8 # arbitrary name of course
| + | |
| − | $ cd ~/biomart_0_8
| + | |
| − | $ svn co <nowiki>https://code.oicr.on.ca/svn/biomart/biomart-java/branches/oct_3_2011</nowiki> # creates "oct_3_2011" directory
| + | |
| − | $ mv oct_3_2011 martconfigurator # friendlier name
| + | |
| − | $ cd martconfigurator
| + | |
| − | $ ant # build project with ant; in the future, you may use: ant clean dist
| + | |
| − | $ ls dist/scripts/martconfigurator.sh dist/scripts/biomart-server.sh # what we care about
| + | |
| − | | + | |
| − | = Building mart =
| + | |
| − | | + | |
| − | This section will show you how to create a (simplified) mart containing 1 dataset based on the VEGA database, using MartBuilder.
| + | |
| − | | + | |
| − | == Describing mart (MartBuilder) ==
| + | |
| − | | + | |
| − | Creating/loading sample mart
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| − | | + | |
| − | === Start MartBuilder ===
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| − | | + | |
| − | From the directory ~/biomart_0>7/martj, issue:
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| − | $ bin/martbuilder.sh
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| − | | + | |
| − | MartBuilder should open with an empty mart.
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| − | | + | |
| − | === Add a schema ===
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| − | | + | |
| − | Choose ''Schema''->''Add'' to open the dialog to add a schema.
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| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | # Name: vega
| + | |
| − | # Database type: MySQL
| + | |
| − | # Using MyISAM: ''checked''
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| − | # Host: localhost
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| − | # Port: 3306
| + | |
| − | # Database: mini_hsap_vega
| + | |
| − | # Schema: mini_hsap_vega
| + | |
| − | # Username: biomart
| + | |
| − | # Password: biomart
| + | |
| − | ''ignore the last 3 fields (used for partitioning which is not covered in this tutorial)''
| + | |
| − | | + | |
| − | [[File:Mb_add_schema2.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | Click the ''Test'' button to ensure we can connect to the database.
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| − | Click the ''Add'' button in order to proceed with the dataset description.
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| − | | + | |
| − | You should now see the source database show in MartBuilder.
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| − | | + | |
| − | '''Note''' that if you did not specify a schema when creating your database, your tables will be in the default schema for your platform:
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| − | # MySQL: has no notion of schema, database acts as a schema
| + | |
| − | # PostGreSQL: ''public''
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| − | # Microsoft SQL Server: ''dbo''
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| − | # Oracle & DB2: the ''username'' of the user who created the database
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| − | | + | |
| − | === Choose dataset ===
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| − | | + | |
| − | We are going to create a dataset based on the tables "gene" and "transcript" (as ''main'' and ''submain'' tables respectively, as described in presentation)
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| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | # Right-click on the "gene" table
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| − | # Click on ''Create dataset''
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| − | ''the gene table should be highlighted already as we arrived on the current menu by clicking on it''
| + | |
| − | # add the transcript table (standard "Ctrl + click)
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| − | # Press the ''Create'' button
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| − | | + | |
| − | [[File:Mb__create_dataset.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | This shows how the dataset will be structured once materialized
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| − | | + | |
| − | [[File:Mb__dataset.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | == Materializing mart (MartBuilder->MartRunner) ==
| + | |
| − | | + | |
| − | Your dataset does not actually exist yet. In order to create it, you need to generate the SQL for it then run that SQL against your database.
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| − | | + | |
| − | BioMart offers a tool (MartRunner) that does that for you, using JDBC. The SQL used is as ANSI-compliant as possible, with some exceptions based on the RDBMS in use.
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| − | | + | |
| − | 1. We now going to transform the source data into target dataset, but before that, we have to create a target database:
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| − | | + | |
| − | $ MY_DESTINATION_DATABASE=mini_hsap_vega_mart
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| − | $ mysql -hlocalhost -P3306 -ubiomart -pbiomart -e "create database $MY_DESTINATION_DATABASE"
| + | |
| − | | + | |
| − | In theory one could materialize a mart in the same database as the source one provided there is no table name conflicts, but this is strongly discouraged.
| + | |
| − | | + | |
| − | Also we have to have MartRunner running. Lets run it over a local port (any free one will do).
| + | |
| − | | + | |
| − | 2. Start martrunner with:
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| − | | + | |
| − | $ MY_MART_RUNNER_PORT=9876
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| − | $ bin/martrunner.sh $MY_MART_RUNNER_PORT
| + | |
| − | | + | |
| − | MartBuilder will send the materialization SQL to MartRunner through that port (in this example, 9876), and MartRunner will execute the transformation SQL.
| + | |
| − | | + | |
| − | Note that MartRunner may be run from another machine, as we specify its connection parameters to MartBuilder (see below).
| + | |
| − | | + | |
| − | We go back to MartBuilder, and click on the ''Build Mart'' button to pop up the following dialog:
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| − | | + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | | + | |
| − | # Datasets: gene
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| − | # Schema partitions: ''ignore''
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| − | # Target database: mini_hsap_vega_mart (the one we just manually created)
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| − | # Target schema: mini_hsap_vega_mart
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| − | # Send SQL to: MartRunner (other options are available)
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| − | # MartRunner host name: localhost
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| − | # MartRunner port number: 9876 (the one we just '''arbitrarily''' chose because it was free)
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| − | # Database server name: localhost
| + | |
| − | # Database server port number: 3306
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| − | | + | |
| − | | + | |
| − | [[File:Mb__build_mart_dialog.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | Click on the ''Generate SQL'' button
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| − | | + | |
| − | [[File:Mb__sql_generation.png]]
| + | |
| − | </div>
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| − | | + | |
| − | 3. Monitor progress using the Monitor MartRunner progress
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | Ensure everything is successful (green font):
| + | |
| − | | + | |
| − | [[File:Mb__job_finished.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | Your schema now contains a mart with a complete dataset ready for configuring with MartConfigurator.
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| − | | + | |
| − | = Configuring mart (MartConfigurator) - basic =
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| − | | + | |
| − | This section will show you how to configure the created VEGA mart using MartConfigurator
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| − | | + | |
| − | | + | |
| − | == Start MartConfigurator ==
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| − | | + | |
| − | Start MartConfigurator with the following command in the directory of your installation:
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| − | | + | |
| − | $ dist/scripts/martconfigurator.sh
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| − | | + | |
| − | | + | |
| − | === Brief intro to the main interfaces of the MC ===
| + | |
| − | | + | |
| − | * screenshot here
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| − | [[File:MCmain.png]]
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| − | | + | |
| − | === Add Mart ===
| + | |
| − | 1. Wizard step 1/4:
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| − | <div class="emphasisbox">
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| − | '''Fill in the fields using the following values:'''
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| − | | + | |
| − | # source profile: vega (''anything will do'')
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| − | # source type: RDBMS Mart
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| − | | + | |
| − | [[File:Mc__add_source_wizard_1.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | 2. Wizard step 2/4:
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| − | <div class="emphasisbox">
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| − | # RDBMS: MySQL (keep MyISAM)
| + | |
| − | # Host: localhost
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| − | # Port: 3306
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| − | # User: biomart
| + | |
| − | # Password: biomart
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| − | # Database: ''can leave empty for now''
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| − | [[File:Mc__add_source_wizard_2.png]]
| + | |
| − | </div>
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| − | | + | |
| − | 3. Wizard step 3/4:
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| − | <div class="emphasisbox">
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| − | Select ''mini_hsap_vega_mart'', the mart that we just built using MartBuilder/MartRunner and based upon the ''mini_hsap_vega'' database
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| − | | + | |
| − | [[File:Mc__add_source_wizard_4.png]]
| + | |
| − | </div>
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| − | | + | |
| − | 4. Wizard step 4/4:
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| − | <div class="emphasisbox">
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| − | # Create naive configuration
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| − | # Choose the main table ''gene__gene__main'' (only one)
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| − | [[File:Mc__add_source_wizard_5.png]]
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| − | </div>
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| − | | + | |
| − | 5. Done!
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| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | You are now '''connected'''!
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| − | | + | |
| − | The panel on the left corresponds to source schemas; in our case we only have one mart that has one dataset: ''mini_hsap_vega_mini'', but there could be more
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| − | | + | |
| − | The panel on the right corresponds to configuration of those source schemas (accessibility, rendering, linking, ...)
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| − | | + | |
| − | [[File:Mc__connected.png]]
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| − | </div>
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| − | | + | |
| − | === Creating Access Point ===
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| − | | + | |
| − | <div class="emphasisbox">
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| − | Simply drag-and-drop the source from the left side (''Source'' frame) to anywhere on the right side (''Portal'' frame)
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| − | | + | |
| − | It will add an access point to the mart. The default name is ''mini_hsap_vega_mart_ap'', ''ap'' standing for ''Access Point'', but you can give it a name of your choice.
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| − | | + | |
| − | Note that clicking the ''Add Access Point'' button would yield the same result. You would then be given a list of the existing marts to choose from.
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| − | | + | |
| − | [[File:Mc__ready.png]]
| + | |
| − | </div>
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| − | | + | |
| − | === Customizing configuration ===
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| − | | + | |
| − | <div class="emphasisbox">
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| − | Double-click on the access point ''mini_hsap_vega_mart_ap'' to bring out the configuration editor (will be detailed in the following section)
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| − | | + | |
| − | [[File:Mc__config.png]]
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| − | </div>
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| − | | + | |
| − | | + | |
| − | === Deploying BioMart Server (Jetty) ===
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| − | | + | |
| − | In order to deploy the application on Jetty, one has 2 options:
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| − | | + | |
| − | * GUI approach: Using the ''Start Server'' button in the upper right corner
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| − | * CLI approach:
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| − | ** Save the the current state (referred to as ''registry'' in MartConfigurator)
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| − | ** Manually start the server:
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| − | $ dist/scripts/biomart-server.sh start
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| − | | + | |
| − | * GUI approach:
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| − | ** Using the ''Start Server'' button will result in prompting a dialog for saving the registry.
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| − | ** The server will be deployed on your local machine, port 9000 by default (unless specified differently in .biomart.properties file).
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| − | ** Your web page should open automatically when the local server is ready.
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| − | | + | |
| − | == Stopping the server ==
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| − | | + | |
| − | * GUI approach: Using the ''Stop Server'' button in the upper right corner
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| − | * CLI approach:
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| − | $ dist/scripts/biomart-server.sh stop
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| − | | + | |
| − | | + | |
| − | === Using deployed application ===
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| − | | + | |
| − | The interface is intuitive, typical interaction involve choose a number of attributes and filters and obtaining results accordingly.
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| − | | + | |
| − | | + | |
| − | = Configuring mart (MartConfigurator) - more advanced =
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| − | | + | |
| − | From the configuration editor (see previous section)
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| − | | + | |
| − | | + | |
| − | == Configuration editor ==
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| − | | + | |
| − | === Description ===
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| − | | + | |
| − | * ''north'': Configuration tree
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| − | ** ''Show sources view'': where one can modify config in a way that will affect all access points
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| − | ** ''Show access point view'': where one can modify individual access point's configs specifically
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| − | ** ''Show both'': most typical usage
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| − | *** ''north west'': source view
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| − | *** ''north east'': access point view
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| − | <div class="emphasisbox">
| + | |
| − | [[File:ConfigurationEditor.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | * ''south'': Editor frame
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| − | ** ''south west'': property names
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| − | ** ''south east'': property values
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| − | | + | |
| − | === Notes ===
| + | |
| − | | + | |
| − | Only properties whose name appears in blue font can be modified.
| + | |
| − | | + | |
| − | Each view as a ''Find'' search box that allows to quickly find attributes/filters based on their names
| + | |
| − | | + | |
| − | Also very convenient, the attributes and filters in each view offer an ''Show in the [opposite view]'' item in their context menu. It filters the opposite view side to show the counterpart filter/attribute
| + | |
| − | | + | |
| − | == Containers ==
| + | |
| − | | + | |
| − | Typical properties that can be changed:
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| − | | + | |
| − | * displayname
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| − | * description
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| − | * hide: whether attribute should be hidden or not
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| − | * enableselectall: offer checkbox allowing selection of all attributes/filters in the given container
| + | |
| − | | + | |
| − | | + | |
| − | == Attributes ==
| + | |
| − | | + | |
| − | Typical properties that can be changed:
| + | |
| − | | + | |
| − | * displayname
| + | |
| − | * description
| + | |
| − | * hide
| + | |
| − | * linkouturl: to make result values linkable to an external resource
| + | |
| − | * datatype: String, Integer, Float, Boolean (useful mostly for reordering)
| + | |
| − | | + | |
| − | | + | |
| − | == Filters ==
| + | |
| − | | + | |
| − | Typical properties that can be changed:
| + | |
| − | | + | |
| − | * displayname
| + | |
| − | * description
| + | |
| − | * type (covered in the next section)
| + | |
| − | * qualifier: whether to use "=", "<=", ">=", "LIKE" operations
| + | |
| − | * spliton: separator for filter list values (see below)
| + | |
| − | | + | |
| − | | + | |
| − | == Filters types ==
| + | |
| − | | + | |
| − | === Regular filters ===
| + | |
| − | | + | |
| − | Typically used to (suprisingly) filter data based on values of interest (for instance a specific gene, or location, or type, ...)
| + | |
| − | | + | |
| − | === Filter lists ===
| + | |
| − | | + | |
| − | They are considered filter themselves, but actually contain a list of regular filters
| + | |
| − | | + | |
| − | | + | |
| − | === Linking ===
| + | |
| − | | + | |
| − | Set Filter typesSet Attribute URLSelect GUI type
| + | |
| − | | + | |
| − | Creating Links between sources
| + | |
| − | | + | |
| − | If two data sources contain common information (e.g. a Gene/Protein ID), this can be used to create a link, allowing filters and attributes from one data source to appear in the other. These are called “pointer attributes” and “pointer filters,” and the attribute or filter to which they point is called the “target. ”To add a pointer to an access point, double click on that access point in the portal tab to edit it. In the top left corner of the editing window, click on the Import from sources button.
| + | |
| − | | + | |
| − | You will be given a list of the existing data sources to choose which one you would like to make an access point for. After giving the new access point a name of your choice, it will appear in the GUI tab.
| + | |
| − | Double-clicking on the access point icon will open a new window that allows you to modify the access point.
| + | |
| − | References
| + | |
| − | | + | |
| − | | + | |
| − | = More exercises with MartConfigurator =
| + | |
| − | | + | |
| − | # Rename 'default' GUI tab to "Form":
| + | |
| − | ## Right-click on the tab --> ''Rename''
| + | |
| − | ## enter new name: "Form"
| + | |
| − | # Add new GUI wizard:
| + | |
| − | ## Click on the "+" sign next to the latest GUI tab (currently just renamed "Form")
| + | |
| − | ## Enter name of the new tab: "Wizard"
| + | |
| − | ## Right-click on the newly created tab --> ''Set GUI type'' --> ''MartWizard''
| + | |
| − | # Use remote mart (URL Mart) Using backward compatibility (from previous BioMart versions: <= 0.7):
| + | |
| − | ## In the ''Source'' view: ''Add Mart'' (see [[Add Mart]])
| + | |
| − | ## Select ''URL Mart'' --> ''Next''
| + | |
| − | ## Input the following values:
| + | |
| − | * Protocol: http
| + | |
| − | * Host: www.biomart.org
| + | |
| − | * Port: 80
| + | |
| − | * Path: /biomart/martservice
| + | |
| − | ## Choose source: vega (url) --> ''Next''
| + | |
| − | *** Select all 3 datasets
| + | |
| − | *** Uncheck ''import each datasets to individual marts, one dataset per mart'' --> ''Finish''
| + | |
| − | | + | |
| − | | + | |
| − | * add vega mart via DB based BC
| + | |
| − | * create an AccessPoint under Form, and another one under Wizard
| + | |
| − | * deploy
| + | |
| − | * exam chromosome filter (singleSelect), gene type filter (multiSelect), how to edit dropdown options for those filters
| + | |
| − | * exam Multiple Chromosomal Regions (Chr:Start:End:Strand) filter
| + | |
| − | * create attribute list
| + | |
| − | * add pathway dataset via URL data source
| + | |
| − | * drag&drop pathway name attribute to vega AP under Form GUI tab, this will trigger link creation (detailed below)
| + | |
| − | * link creation between pathway and vega gene. use ensembl gene id as the attribute/filter pair to build the link
| + | |
| − | * deploy the server and select pathway name together with other attribute from vega gene dataset, exam the result
| + | |
| − | * drag&drop pathway name filter to vega AP under Wizard GUI tab, then deploy the sever and choose pathway filter then exam result
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| − | = Querying a BioMart server via REST API =
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| − | == MetaData queries ==
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| − | http://localhost:9000/martservice/marts
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| − | http://localhost:9000/martservice/datasets?mart=gene_vega
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| − | http://localhost:9000/martservice/accesspoints?datasets=&mart=gene_vega
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| − | http://localhost:9000/martservice/attributes?dataset=hsapiens_gene_vega&mart=gene_vega
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| − | http://localhost:9000/martservice/filters?dataset=hsapiens_gene_vega&mart=gene_vega
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| − | == Data query ==
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| − | <xml>
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| − | <Query processor="TSV" header="true" limit="-1" client="webbrowser">
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| − | <Dataset name="hsapiens_gene_vega" config="gene_vega_ap">
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| − | <Filter name="chromosomal_region" value="2:1000000:2000000:1,4:9000000:11000000:-1"/>
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| − | <Filter name="biotype" value="protein_coding"/>
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| − | <Attribute name="vega_gene_id"/>
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| − | <Attribute name="vega_transcript_id"/>
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| − | <Attribute name="vega_translation_id"/>
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| − | <Attribute name="chromosome_name"/>
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| − | <Attribute name="start_position"/>
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| − | <Attribute name="end_position"/>
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| − | <Attribute name="strand"/>
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| − | <Attribute name="band"/>
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| − | </Dataset>
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| − | </Query>
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| − | </xml>
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| − | Paste this piece of XML in a web browse address as:
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| − | http://localhost:9000/martservice/results?query=paste_query_xml_string_here
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| − | To read more about BioMart, refer to the recent articles describing the BioMart software and its applications.
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| − | 1. Zhang J, Haider S, Baran J, Cros A, Guberman JM, Hsu J, Liang Y, Yao L, Kasprzyk A. BioMart: a data federation framework for large collaborative projects. Database (Oxford). 2011 Sep 19:2011:bar038.
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| − | 2.Guberman JM, Ai J, Baran J., et al. BioMart Central Portal: An Open Database Network for the Biological Community. Database (Oxford). 2011 Sep18;2011:bar041.
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| − | 3. Zhang J, Baran J, Guberman JM, Haider, S, Hsu J, Liang Y, Rivkin E, Wang J, Whitty B, Wong-Erasmus M, Yao L, Kasprzyk A. International Cancer Genome Consortium Data Portal - a One-stop Shop for Cancer Genomics Data. Database (Oxford). 2011 Sep19;2011:bar026.
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| | [[Category:BioMart]] | | [[Category:BioMart]] |
