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| − | {| class="tutorialheader"
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| − | | 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 />
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| − | [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 />
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| − | 14 October 2011<br />
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| − | [[User:Junjun|Junjun Zhang]], [[User:Elena%20Rivkin|Elena Rivkin]] and [[User:Anthony%20Cros|Anthony Cros]]
| |
| − | |}
| |
| | __NOTITLE__ | | __NOTITLE__ |
| | | | |
| − | | + | <center>{{#icon: Biomart250.png|BioMart||http://www.biomart.org/}}</center> |
| − | This tutorial walks you through how to install and configure a local installation of [[BioMart]].
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | = 1. Setting up the virtual machine =
| + | |
| − | | + | |
| − | == 1.1 Import and start the VM ==
| + | |
| − | * We have create a virtual machine (VM) image using Oracle's VirtualBox software tool. The image file is in OVF/OVA format, you should be able to set up the VM using VirtualBox or VMware player. At this time, you should have one of them installed already.
| + | |
| − | * We will be passing around USB memory sticks that contain the image file, please copy it to your laptop.
| + | |
| − | * Import and start the VM using VirtualBox:
| + | |
| − | ** Start VirtualBox
| + | |
| − | ** Import image with: (from the menu bar) File --> Import Appliance
| + | |
| − | ** Navigate to the .ova file you just copied from the USB key and follow on screen instructions
| + | |
| − | ** After imported, choose to start the VM by clicking the Start button
| + | |
| − | | + | |
| − | == 1.2 Accounts that you will need for this tutorial ==
| + | |
| − | * Linux:
| + | |
| − | ** username: biomart
| + | |
| − | ** pasword: biomart
| + | |
| − | | + | |
| − | * MySQL:
| + | |
| − | ** username: biomart
| + | |
| − | ** pasword: biomart
| + | |
| − | | + | |
| − | In order to free up some disk space you will need to drop some unneeded databases:
| + | |
| − | mysql -ubiomart -pbiomart -e "drop database vega_mart_58_template"
| + | |
| − | mysql -ubiomart -pbiomart -e "drop database homo_sapiens_vega_58_37c"
| + | |
| − | mysql -ubiomart -pbiomart -e "drop database vega_mart_63"
| + | |
| − | | + | |
| − | = 2. Downloading & Installing BioMart =
| + | |
| − | | + | |
| − | Two components are necessary for this tutorial: MartBuilder from an older version of BioMart release (0.7), and MartConfigurator is from the most recent development code snapshot (0.8)
| + | |
| − | | + | |
| − | 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 it yourself in the tutorial.
| + | |
| − | | + | |
| − | == 2.1 Installing Biomart 0.7 - MartJ package ==
| + | |
| − | | + | |
| − | MartJ contains applications necessary to create a Mart: MarBuilder and MartRunner.
| + | |
| − | | + | |
| − | Download & extract tarball content with:
| + | |
| − | | + | |
| − | $ cd
| + | |
| − | $ mkdir biomart_0_7
| + | |
| − | $ cd biomart_0_7
| + | |
| − | $ wget <nowiki>ftp://anonymous@ftp.ebi.ac.uk/pub/software/biomart/martj_current/martj-bin.tgz</nowiki>
| + | |
| − | $ tar zxvf martj-bin.tgz # creates "martj-0.7" directory
| + | |
| − | $ cd martj-0.7
| + | |
| − | | + | |
| − | == 2.2 Installing Biomart 0.8 ==
| + | |
| − | | + | |
| − | Checkout a specific revision of the current development code from SVN repository as below:
| + | |
| − | | + | |
| − | $ cd
| + | |
| − | $ mkdir biomart_0_8
| + | |
| − | $ cd biomart_0_8
| + | |
| − | $ svn co <nowiki>-r 10500 https://code.oicr.on.ca/svn/biomart/biomart-java/branches/oct_3_2011 martconfigurator</nowiki>
| + | |
| − | $ cd martconfigurator
| + | |
| − | $ ant # build project with ant; in the future, you may use: ant clean dist
| + | |
| − | | + | |
| − | = 3. Building mart =
| + | |
| − | | + | |
| − | This section will show you how to create a mart database from a normal relational database using MartBuilder. We use a simplified VEGA database as a start.
| + | |
| − | | + | |
| − | == 3.1 Creating mart schema using MartBuilder ==
| + | |
| − | | + | |
| − | === 3.1.1 Start MartBuilder ===
| + | |
| − | | + | |
| − | | + | |
| − | $ cd ~/biomart_0_7/martj-0.7
| + | |
| − | $ bin/martbuilder.sh
| + | |
| − | | + | |
| − | MartBuilder should open (see screenshot below):
| + | |
| − | [[File:Mbuilder07.png]]
| + | |
| − | | + | |
| − | === 3.1.2 Add a source schema ===
| + | |
| − | | + | |
| − | In the menu bar, choose ''Schema''->''Add'' to open the dialog to add a schema.
| + | |
| − | | + | |
| − | Fill in the fields with the follow values as shown in the screenshot below:
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | # Name: vega
| + | |
| − | # Database type: MySQL
| + | |
| − | # Using MyISAM: ''checked''
| + | |
| − | # Host: localhost
| + | |
| − | # 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.
| + | |
| − | Click the ''Add'' button in order to proceed with the dataset description.
| + | |
| − | | + | |
| − | You should now see the source database shown in MartBuilder as below:
| + | |
| − | <div class="emphasisbox">
| + | |
| − | [[File:MbSourceSchema.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | === 3.1.3 Select main table(s) and generate mart schema ===
| + | |
| − | | + | |
| − | We are going to create a dataset based on the tables "gene" and "transcript" (as ''main'' and ''submain'' tables respectively, as described in presentation)
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | # Right-click on the "gene" table
| + | |
| − | # Click on ''Create dataset''
| + | |
| − | ''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)
| + | |
| − | # Press the ''Create'' button
| + | |
| − | | + | |
| − | [[File:Mb__create_dataset.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | This shows the mart schema (reverse star) of the dataset that has been just create.
| + | |
| − | | + | |
| − | [[File:Mb__dataset.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | == 3.2 Materializing the mart ==
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | 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. | + | |
| − | | + | |
| − | === 3.2.1 Preparing database and start MartRunner ===
| + | |
| − | | + | |
| − | * We now going to transform the source data into target dataset, but before that, we have to create a target database:
| + | |
| − | | + | |
| − | $ mysql -hlocalhost -P3306 -ubiomart -pbiomart -e "create database mini_hsap_vega_mart"
| + | |
| − | | + | |
| − | * Start MartRunner using port 9876 with:
| + | |
| − | | + | |
| − | $ cd ~/biomart_0_7/martj-0.7/
| + | |
| − | $ bin/martrunner.sh 9876
| + | |
| − | | + | |
| − | MartBuilder will send the materialization SQL to MartRunner through that port (in this example, 9876), and MartRunner will execute the transformation SQL.
| + | |
| − | | + | |
| − | === 3.2.2 Starting schema transformation from MartBuilder ===
| + | |
| − | | + | |
| − | We go back to MartBuilder, and click on the ''Build Mart'' button to pop up the following dialog:
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | | + | |
| − | # Datasets: gene
| + | |
| − | # Schema partitions: ''ignore''
| + | |
| − | # Target database: mini_hsap_vega_mart (the database we just manually created)
| + | |
| − | # Target schema: mini_hsap_vega_mart (same as database for MySQL)
| + | |
| − | # Send SQL to: MartRunner
| + | |
| − | # MartRunner host name: localhost
| + | |
| − | # MartRunner port number: 9876 (the one we just '''arbitrarily''' chose because it was free)
| + | |
| − | # Database server name: localhost
| + | |
| − | # Database server port number: 3306
| + | |
| − | | + | |
| − | | + | |
| − | [[File:Mb__build_mart_dialog.png]]
| + | |
| − | | + | |
| − | Click on the ''Generate SQL'' button
| + | |
| − | | + | |
| − | </div>
| + | |
| − | | + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | | + | |
| − | [[File:Mb__sql_generation.png]]
| + | |
| − | | + | |
| − | Click on the "Start job" button
| + | |
| − | </div>
| + | |
| − | | + | |
| − | === 3.2.3 Monitoring MartRunner transformation progress ===
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | | + | |
| − | [[File:Mb__job_finished.png]]
| + | |
| − | | + | |
| − | Ensure everything is successful, ie, displayed in green font!
| + | |
| − | | + | |
| − | </div>
| + | |
| − | | + | |
| − | You now have a mart database created from a 3NF normalized source database, and it's ready for configuring using MartConfigurator.
| + | |
| − | | + | |
| − | = 4. Configuring a data portal to expose the mart using MartConfigurator =
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | | + | |
| − | This section will show you how to use MartConfigurator to configure a data portal web server that exposes the created VEGA mart to end users for querying.
| + | |
| − | | + | |
| − | </div>
| + | |
| − | | + | |
| − | == 4.1 Start MartConfigurator ==
| + | |
| − | | + | |
| − | Start MartConfigurator with the following command:
| + | |
| − | | + | |
| − | $ cd ~/biomart_0_8/martconfigurator
| + | |
| − | $ dist/scripts/martconfigurator.sh
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | The panel on the left corresponds to data sources; in our case we will add the mart that has been just created: ''mini_hsap_vega_mart''
| + | |
| − | | + | |
| − | The panel on the right corresponds to access points for those data sources that will be exposed to web users.
| + | |
| − | | + | |
| − | [[File:mc__empty.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | == 4.2 Add our own mart: mini_hsap_vega_mart ==
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | Click on the ''Add Mart'' button to add a datasource
| + | |
| − | | + | |
| − | [[File:Mc__add_mart__button.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | * Wizard step 1 of 4:
| + | |
| − | <div class="emphasisbox">
| + | |
| − | # source profile: vega (''anything will do'')
| + | |
| − | # source type: RDBMS Mart
| + | |
| − | | + | |
| − | [[File:Mc__add_source_wizard_1.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | * Wizard step 2 of 4:
| + | |
| − | <div class="emphasisbox">
| + | |
| − | # RDBMS: MySQL (keep MyISAM checked)
| + | |
| − | # Host: localhost
| + | |
| − | # Port: 3306
| + | |
| − | # User: biomart
| + | |
| − | # Password: biomart
| + | |
| − | # Database: ''can leave empty for now''
| + | |
| − | [[File:Mc__add_source_wizard_2.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | * Wizard step 3 of 4:
| + | |
| − | <div class="emphasisbox">
| + | |
| − | | + | |
| − | Select ''mini_hsap_vega_mart'', the mart that we just built using MartBuilder/MartRunner and based upon the ''mini_hsap_vega'' database
| + | |
| − | | + | |
| − | [[File:Mc__add_source_wizard_4.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | * Wizard step 4 of 4:
| + | |
| − | <div class="emphasisbox">
| + | |
| − | # Create naive configuration
| + | |
| − | # Choose the main table "gene__gene__main"
| + | |
| − | | + | |
| − | [[File:AddSourceWizard4.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | * Now we should have our own mart added
| + | |
| − | | + | |
| − | == 4.3 Creating Access Point ==
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | Simply drag-and-drop the mart from the left side (''Source'' panel) to anywhere on the right side (''Portal'' panel).
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | Note that you can also create an access point by clicking the ''Add Access Point'' button. You would then be given a list of the existing marts to choose from.
| + | |
| − | | + | |
| − | [[File:Mc__ready.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | == 4.4 Deploying the data portal, ie, the BioMart Server ==
| + | |
| − | | + | |
| − | To deploy the web based data portal, simply click on '''Start Server''' button on the top right corner.
| + | |
| − | | + | |
| − | * When the '''Start Server''' button is click, if the current configuration (registry) has never been save, you will be prompted with a dialog for saving the current ''registry''.
| + | |
| − | * Save the registry under /home/biomart/biomart_0_8/martconfigurator/registry/
| + | |
| − | * The data portal will be deployed on your local machine using port 9000 by default.
| + | |
| − | * Your web browser should open and pointing to http://localhost:9000/ automatically when the server is ready.
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | * Note the URL: localhost:9000/web (default)
| + | |
| − | [[File:Mc__deployed_server.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | | + | |
| − | * To stop the server use the ''Stop Server'' button in the upper right corner
| + | |
| − | | + | |
| − | There is also a command-line approch to starting/stopping the server using:
| + | |
| − | $ dist/scripts/biomart-server.sh start
| + | |
| − | $ dist/scripts/biomart-server.sh stop
| + | |
| − | but that will not be covered here.
| + | |
| − | | + | |
| − | == 4.5 Exploring our first BioMart data portal ==
| + | |
| − | | + | |
| − | You can choose some attributes and hit "GO" button to get some result.
| + | |
| − | | + | |
| − | = 5. More MartConfigurator exercises =
| + | |
| − | | + | |
| − | MartConfigurator is a desktop application for configuring a data portal (ie, a BioMart Server).
| + | |
| − | | + | |
| − | == 5.1 The MartConfigurator main window ==
| + | |
| − | | + | |
| − | As it's shown before, the main window is divided into left and right halves. Left for managing data sources and right for managing access points. Access point is how a data source is presented to the end user for querying from web GUI or an API client.
| + | |
| − | | + | |
| − | There are two main activities at the main window:
| + | |
| − | * adding data sources
| + | |
| − | * adding/configuring data access points
| + | |
| − | | + | |
| − | Configuring a source or an access point mainly involves creating Attributes and Filters, and organizing them into containers (and sub-containers)
| + | |
| − | | + | |
| − | Double-click a mart icon in the Source panel or an access point icon on the Portal panel will bring up the ConfigurationEditor window (next section for details).
| + | |
| − | | + | |
| − | == 5.2 ConfigurationEditor window ==
| + | |
| − | | + | |
| − | * '''Left''' panel: Source Config
| + | |
| − | * '''Right''' panel: Access Point
| + | |
| − | * Both panels are similarly divided into top and bottom sections
| + | |
| − | ** top section showing the containers and their containing attributes or filters
| + | |
| − | ** bottom section showing the properties and its values for a selected configuration items: container, attribute or filter
| + | |
| − | | + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | [[File:ConfigurationEditor.png]]
| + | |
| − | | + | |
| − | * Only properties whose name appears in blue font can be modified.
| + | |
| − | | + | |
| − | * Each view has 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
| + | |
| − | | + | |
| − | * By drag-and-drop from the left to right, we can add new attributes/filters from a source to its access point
| + | |
| − | | + | |
| − | </div>
| + | |
| − | | + | |
| − | == 5.3 Rename '''default''' GUI tab to '''Form''' ==
| + | |
| − | # GUI tab (or GUI container) is used to organize access points, it usually corresponds to a box on the home page of the data portal.
| + | |
| − | # Right-click on the tab --> ''Rename''
| + | |
| − | # enter new name: "Form"
| + | |
| − | | + | |
| − | == 5.4 Add new GUI tab ==
| + | |
| − | # Click on the "+" sign next to the latest GUI tab
| + | |
| − | # Enter name of the new tab: "Wizard"
| + | |
| − | # Right-click on the newly created tab --> ''Set GUI type'' --> ''MartWizard''
| + | |
| − | | + | |
| − | == 5.5 Add full VEGA mart: an external URL-based mart source ==
| + | |
| − | | + | |
| − | # Add remote mart (URL Mart) Using backward compatibility (from previous BioMart versions: <= 0.7)
| + | |
| − | # In the ''Source'' view: ''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 and click ''Next''
| + | |
| − | # Uncheck ''import each datasets to individual marts, one dataset per mart'' --> ''Finish''
| + | |
| − | #* Backward compatibility is run in the background in order to convert a mart configuration in 0.7 format to one in 0.8
| + | |
| − | # A datas ource called "gene_vega" should appear on the right-hand side panel (datasource panel)
| + | |
| − | | + | |
| − | == 5.6 Add Pathway dataset from REACTOME mart: another external URL-based mart source ==
| + | |
| − | | + | |
| − | | + | |
| − | * Reproduce the same process in previous section excepted for step 5 where we choose "REACTOME (url)", then in step 6 we select '''pathway''' only
| + | |
| − | | + | |
| − | == 5.7 Add access points for the gene_vega URL mart ==
| + | |
| − | | + | |
| − | # Choose the "Form" GUI tab
| + | |
| − | # Drag-and-drop the "vega_gene" mart from the left to the portal panel
| + | |
| − | # Rename the new access point to "VEGA Genes in MartForm" by right-click the access point icon
| + | |
| − | # Choose the "Wizard" GUI tab
| + | |
| − | # Drag-and-drop the "vega_gene" mart from the left to the portal panel
| + | |
| − | # Rename the new access point to "VEGA Genes in MartWizard" by right-click the access point icon
| + | |
| − | | + | |
| − | == 5.8 Re-deploy server ==
| + | |
| − | | + | |
| − | * Now re-deploy the server using "Start Server" button. If the server is running already, stop it first.
| + | |
| − | * Check it out in web browser, how different GUI type offers different query interfaces
| + | |
| − | | + | |
| − | == 5.9 Change settings to attribute ==
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | * Understand and fix the linkouturl setting for VEGA gene ID:
| + | |
| − | [[File:Linkouturl.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | * To fix it, we need to change the pseudoattribute ''exturl'' value to: <nowiki>http://www.ensembl.org</nowiki>
| + | |
| − | [[File:EditPseudoAtt.png]]
| + | |
| − | </div>
| + | |
| − | | + | |
| − | == 5.10 Understanding filter types ==
| + | |
| − | | + | |
| − | # Double-click the 'gene_vega' mart icon to open ConfigurationEditor window
| + | |
| − | # Click the 'Show both' button on the top
| + | |
| − | # Find the follow filters by typing their name in the Find text box
| + | |
| − | #* singleSelect type: "Chromosome"
| + | |
| − | #* multiSelect: "Gene type"
| + | |
| − | # To edit the dropdown content of the above filter:
| + | |
| − | #* right-click the filter and choose ''Dropdown options''
| + | |
| − | | + | |
| − | == 5.11 Importing attributes/filters from external mart ==
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | The task: generate a gene list by specifying the pathway name in which the genes are involved.
| + | |
| − | </div>
| + | |
| − | | + | |
| − | <div class="emphasisbox">
| + | |
| − | The solution: drag-and-drop 'pathway name' filter from 'pathway' to a 'gene_vega' access point
| + | |
| − | </div>
| + | |
| − | | + | |
| − | '''Here is how:'''
| + | |
| − | [[File:CreatePointerFilter.png]]
| + | |
| − | | + | |
| − | '''Before that you will need to create a link between the two related mart: pathway and gene_vega. Here they are linked through the common Ensembl Gene ID'''
| + | |
| − | [[File:LinkCreation.png]]
| + | |
| − | | + | |
| − | | + | |
| − | '''Now save the changes, "Stop Server" then "Start Server" in MartConfigurator, go to the web browser and exam the query interface. You should see the "Miscellaneous - Pathway Name" filter under VEGA Gene. Try select a pathway name from the dropdown list, and select some attributes for the output genes, it should return the gene involved in the chosen pathway.'''
| + | |
| − | | + | |
| − | = 6. Querying a BioMart server via REST API =
| + | |
| − | | + | |
| − | == 6.1 MetaData queries ==
| + | |
| − | | + | |
| − | http://localhost:9000/martservice/marts
| + | |
| − | | + | |
| − | http://localhost:9000/martservice/datasets?mart=gene_vega
| + | |
| − | | + | |
| − | http://localhost:9000/martservice/accesspoints?datasets=&mart=gene_vega
| + | |
| − | | + | |
| − | http://localhost:9000/martservice/attributes?dataset=hsapiens_gene_vega&mart=gene_vega
| + | |
| − | | + | |
| − | http://localhost:9000/martservice/filters?dataset=hsapiens_gene_vega&mart=gene_vega
| + | |
| − | | + | |
| − | == 6.2 Data query ==
| + | |
| − | | + | |
| − | <xml>
| + | |
| − | <Query processor="TSV" header="true" limit="-1" client="webbrowser">
| + | |
| − | <Dataset name="hsapiens_gene_vega" config="gene_vega_ap">
| + | |
| − | <Filter name="chromosomal_region" value="2:1000000:2000000:1,4:9000000:11000000:-1"/>
| + | |
| − | <Filter name="biotype" value="protein_coding"/>
| + | |
| − | <Attribute name="vega_gene_id"/>
| + | |
| − | <Attribute name="vega_transcript_id"/>
| + | |
| − | <Attribute name="vega_translation_id"/>
| + | |
| − | <Attribute name="chromosome_name"/>
| + | |
| − | <Attribute name="start_position"/>
| + | |
| − | <Attribute name="end_position"/>
| + | |
| − | <Attribute name="strand"/>
| + | |
| − | <Attribute name="band"/>
| + | |
| − | </Dataset>
| + | |
| − | </Query>
| + | |
| − | </xml>
| + | |
| − | | + | |
| − | Paste this piece of XML in a web browse address as:
| + | |
| − | | + | |
| − | http://localhost:9000/martservice/results?query=paste_query_xml_string_here
| + | |
| − | | + | |
| − | or run the follow perl code:
| + | |
| − | | + | |
| − | <pre>
| + | |
| − | #!/usr/bin/perl
| + | |
| − | | + | |
| − | # an example script demonstrating the use of BioMart webservice
| + | |
| − | use strict;
| + | |
| − | use LWP::UserAgent;
| + | |
| − | | + | |
| − | open (FH,$ARGV[0]) || die ("\nUsage: perl webExample.pl Query.xml\n\n");
| + | |
| − | | + | |
| − | my $xml;
| + | |
| − | while (<FH>){
| + | |
| − | $xml .= $_;
| + | |
| − | } | + | |
| − | close(FH);
| + | |
| − | | + | |
| − | my $outfile = $ARGV[1];
| + | |
| − | open (OUT, "> $outfile") if ($outfile);
| + | |
| − | | + | |
| − | my $path="http://localhost:9000/martservice/results?";
| + | |
| − | my $request = HTTP::Request->new("POST",$path,HTTP::Headers->new(),'query='.$xml."\n");
| + | |
| − | my $ua = LWP::UserAgent->new;
| + | |
| − | | + | |
| − | my $response;
| + | |
| − | | + | |
| − | $ua->request($request,
| + | |
| − | sub{
| + | |
| − | my($data, $response) = @_;
| + | |
| − | if ($response->is_success) {
| + | |
| − | $outfile ? print OUT "$data" : print "$data";
| + | |
| − | }
| + | |
| − | else {
| + | |
| − | warn ("Problems with the web server: ".$response->status_line);
| + | |
| − | }
| + | |
| − | },1000);
| + | |
| − | | + | |
| − | close(OUT) if ($outfile);
| + | |
| − | </pre> | + | |
| − | | + | |
| − | on the command line as:
| + | |
| − | | + | |
| − | perl webQuery.pl query.xml
| + | |
| − | | + | |
| − | = 7. Further readings =
| + | |
| − | | + | |
| − | To read more about BioMart, refer to the recent articles describing the BioMart software and its applications.
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | 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.
| + | |
| | | | |
| | [[Category:BioMart]] | | [[Category:BioMart]] |
| | [[Category:Tutorials]] | | [[Category:Tutorials]] |
