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BioMart 0.8 User Manual

1. Clicking the Get button will connect to your database server and show a list of available schemas in the left panel Select a schema to show a list of available tables Note that if you did not specify a schema when creating your database your tables will be in the default schema for your platform MySQL does not have schema will be the same as the database name PostGreSQL public Oracle and DB2 the username of the user who created the database SQL Server dbo bios smart 18 Database type W Using MyISAM 9 Source Schema Relational Mart Host ensembldb ensembl org Port 5306 Database OO EEEE Username anonymous Password Ir 1 f partitioned f homo sapiens vega 49 36k A stable id event f homo sapiens vega 50 36l e Gees If f homo sapiens vega 51 36m I mu f homo sapiens vega 52 36n Mini H f homo sapiens vega 53 360 m Wee ee id g homo_sapiens_vega_54_36p C transcript supporting feature f homo sapiens vega 55 37 homo sapiens vega 56 37a f C translation attrib f homo sapiens vega 57 37b C translation stable id f homo sapiens vega 58 37c o C unconventional_transcript_association f homo sapiens vega 59 37d unmapped_object f homo sapiens vega 60 37e f unmapped_reason vd homo_sapiens_vega_61_37f C xref In the right panel select the table s that will become you main table s and click Add to create your data source
2. 11 4 SOAP API The SOAP API is built on top of the Java API for XML Web Services JAX WS To access the SOAP API you will need tools to help you generate the BioMart SOAP client in the programming language of your choice The WSDL can be accessed at the URL martsoap wsdl In this section we will assume the SOAP service is deployed to http localhost 9000 martsoap with the corresponding WSDL file at http localhost 9000 martsoap wsdl If this is not the case please change the URLs accordingly 11 4 1 Accessing SOAP API Using Java Java 5 and newer comes installed with a tool called wsimport which will build all the client classes needed to interact with a SOAP API mkdir biomartclient amp amp cd biomartclient wsimport http localhost 9000 martsoap wsdl bios smart 76 This will create the class files and their packages under the biomartclient directory You can now use the generated classes to access the SOAP Server Now create the BioMartSoapClient class that performs some data access under the biomartclient directory BioMartSoapClient java import org biomart api soap BioMartSoapService import org biomart api soap PortalServiceImpl import org bromart api soap Mart import org biomart api soap Dataset import org biomart api soap Attribute public class BioMartSoapClient public static void maini sStrinel args BioMartSoapService service new BioMartSoapService PortalServicelmpl port ser
3. keytool genkey keystore keystore alias biomart keyalg RSA You will be prompted to enter a password enter the password you set in the ssl password property in the previous step You will then be prompted for your first and last name Instead enter in your full server address e g www yourserver com You will then be asked for several more pieces of information you can leave them all blank When prompted if the data are all correct type yes Finally you will be asked for another password simply hit enter to use the same password you set earlier 8 2 Authenticated remote access Controlled access for certain authenticated users can be configured in the user management dialogue described in section 5 13 To enable this biossgsmart 46 authentication for server to server communications follow the following procedure which allows Server A to securely retrieve data from Server B On Server B access the web based administration interface located at www serverB com admin where www serverB com is the web address of Server B You will be prompted for a username and password which is configured in the file realm properties located in the web etc subdirectory of the BioMart installation directory By default the username is martadmin and the password is P 2ssword The administration page has an Add New Consumer button which will allow you to create an access token for Server A BioMart Administration
4. bios Smart 19 5 5 Manipulating a Mart using the Schema Editor Various properties of a virtual mart can be customized by right clicking on the source and choosing Schema Editor This will bring up the Schema Editor window source target Hide masked dependent xref homo sapiens vega 61 37 exon transcript mo sapiens vega 61 37f Y ature i density feature o sapiens vega 61 37 v A homo sapiens vega 61 37 i Showcolumns S bel V H y dna_align_feature gt mm CA e homo sapiens vega 61 221 an dnac homo sapiens vega 61 37 jexon V A external_synonym E homo sapiens vega 61 371 y V4 homo sapiens vega 61 371 Se 1 X J Show columns II AANI Show columns EE nn d dna L D m homo sapiens vega 61 271 mapping session trimisc set homo sapiens vega 61 37 homo sapien Aw Show columns Show columns Show columns EL f Show columns Show c tnt c c EE b GD5IAAGAZ 8 reesei The Schema Editor shows database tables pink boxes as well as the relations between these tables connecting lines The columns in a given table can be shown by clicking the Show columns button for that table A table column or relation can be hidden by right clicking on the obj
5. 1 0 gt lt BioMart XML Query Query client webbrowser processor SPARQLXML Limit 1 header 0 gt lt Dataset name hsapiens gene ensembl config my access point gt Filter name chromosome name value X gt Filter name with entrezgene value only gt Attribute name ensembl gene id Attribute name entrezgene lt Dataset gt lt Query gt inne sparql xmlns http www w3 org 2005 sparql results gt lt head gt variable name a0Q gt variable name a1 lt head gt results result binding name aQ gt lt literal gt ENSG00000102128 lt literal gt gios Marl 84 lt binding gt binding name al literal 282808 literal lt binding gt lt result gt lt result gt lt binding name a0 gt literal ENSG00000133169 literal lt binding gt binding name al literal 55859 literal lt binding gt lt result gt and so on lt results gt lt sparql gt 11 6 Java API The Java API provides public methods to communicate with the local registry To use the Java API you must first generate a local XML registry file to load from 11 6 1 MartRegistryFactory The org biomart api factory MartRegistryFactory interface declares the method getRegistry which will return the org biomart api lite MartRegistry object that will be needed in order to interact with the local registry The only implementation currently avail
6. A2 DIMERIC L VITAGLIANO S ADINOLFI A RICCIO F SICA A ZAGARI L MAZZARELLA 3 10 130 10 3 A A 124 3 1 27 5 Single crystal X ray diffraction 30 0003676 GO 0003824 GO 0004518 HYDROLASE GO 0004519 GO 0004522 GO 0016787 IPROO1427 biossgsmart 30 5 10 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 mport from sources button gt Import from sources 0 Search fa om gt 6 root The window will divide into two similar halves The right side represents the access point you are editing and left side lists all of the sources biossgsmart 31 4 Hide sources DP Search IS v Di root v amp ATTRIBUTES v t Features v GENE v H Vega VEGA gene ID 2 VEGA transcript ID VEGA protein ID Canonical transcript stable ID Description Chromosome Name Gene Start bp Gene End bp Strand Band Transcript Start bp Transcript End bp D e Le Ap Source Homo sapiens gene
7. OAUTH CONSUMERS None Add New Consumer TT Powered by biossssmart ee Add OAuth Consumer Name required Description Key required 401f91ac325157aaf03c1408e387a7bf Secret required 0a2b4eBcB618224b3aa4dcBab293cBac245e3e57 Callback You can enter any name you like the important information is the two strings of letters and numbers called Key and Secret You must also authorize the user or users by clicking on the Add access token for user button and following the on screen instructions bios smart AT BioMart Administration OAUTH CONSUMERS x SERVER A Description Key 2d25dc8bb022ce496d23f8d8ac95a815 Secret 7ce4ab04ad4ad3ad1dde6c3b6a24f9a558fa4d0a Add New Consumer ee Powered by Diossssmart Once you have completed the authorization process a dialogue such as the following will be displayed Successfully retrieved access token The client will need all of the following Consumer key 2d25dc8bb022ce496d23f8d8ac95a815 Consumer secret 7ce4ab04ad4ad3ad1 dde6c3b6a24f9a558fa4d0a Access token ab83d6b086163a04a506ee1f3a3d767de Access token secret 9e2e908754dce0a0d40dc277f374d1f7 Close You must combine these four strings separated by commas So in this case it would be 2d25dc8bb022ce496d23f8d8ac95a815 7ce4ab04ad4ad3ad1dde6c3b6a24f9a558fa4dO0a ab 83d6b086163a04a506ee1f3a3d767de 9e2e908754dce0a0d40dc2771f374d1f7 Note tha
8. Sample URL martservice portal guitype2martform Sample XML Response lt guiContainer guiType isHidden false description displayName root lt guiContainers gt name root lt guiContainer guiType martform isHidden false description default displayName default name default gt lt Marts SE GGonfig sup contig isHidden ialse meta operation MULTISELECT desCription senp Contig displayName snp config name snp config gt lt marts gt lt guiContainer gt lt guiContainers gt lt guiContainer gt Sample JSON Response isHidden false GulConteaners isHidden false guiContainers marts isHidden false displayName snp config config snp Contig operation MULTISELECT meta name snp Conia description snp Coniig bios smart 67 quairype s martrtorm name default displayName default description default by Marts quiType s WM hame FOOL displayName root description s Ww 11 3 3 2 Marts Lists all the Marts available from the server URL martservice marts Method GET Parameters guicontainer optional Restricts the returned Marts to the specified GUI Container Returns List of Mart objects Sample URL martservice marts Sample XML Response lt marts gt mart contfig snp config uisHidden rIalse meta
9. Variation Summary v s value Ww attributes 11 3 3 6 Containers Lists all Containers for the given Mart starting from the root Container Note containers and GUI containers are different URL martservice containers Method GET Parameters datasets required Comma separated string of datasets config optional The name of the config as returned by the Mart object You should provide this when the Mart s config is non empty withattributes optional If true containers with Attributes or descendent Containers with Attributes will be included Default is true withfilters optional If true Containers with Filters or descendent Containers with Filters will be included Default is true Returns List of Container objects Sample URL martservice containers datasets btaurus snp amp configzsnp config bios smart 72 Sample XML Response container independent false maxAttributes 0 maxContainers 0 description root displayName root name root gt lt containers gt container independent false maxAttributes 0 maxContainers 0 description NULL displayName Variation Information name Snpsatts gt lt attribute isHidden false Oo O linkURL species2 Variation Summary v s value description displayName Variation ID name rersnp id lt attributes gt attribute container containers container Sample JSON Response nam
10. ant is not a program To install the latest version of Ant please visit the website http ant apache org 12 2 Testing Environment This BioMart 0 8 release candidate is known to work with the following software environments Operating systems Mac OS X Leopard and Snow Leopard Linux Debian 4 1 1 21 Web browsers Firefox 3 6 Microsoft IE 7 Google Chrome 8 0 Safari 5 0 bios smart 95
11. operation MULTISELECT description snp config displayName snp config name snp config lt marts gt Sample JSON Response bios smart 68 isHidden false displayName snp conriig gonrsg s senp COnLLg Operation MULTISELECT meta 9 name snp cOniig description snp Contig by 11 3 3 3 Datasets Lists all the Datasets for the given Mart URL martservice datasets Method GET Parameters mart required The name of the Mart to return datasets from Returns List of Dataset objects Sample URL martservice datasets mart snp_config Sample XML Response lt datasets gt dataset LisHidden ralse description btaurus snp displayName Bos taurus Variation dbSNP 130 name btaurus snp lt datasets gt Sample JSON Response isHidden false name s DECAUPTUS Shp displayName Bos taurus Variation dbSNP 130 description breusus snp by bios smart 69 11 3 3 4 Filters Lists all the filters for the given Dataset s URL martservice filters Method GET Parameters datasets required Comma separated string of Datasets config optional The name of the config as returned by the Mart object You should provide this when the Mart s config is non empty container optional The name of the container you want to return filters for Returns List of filter objects Sample URL martservice filters datasets btaurus
12. 0 Oo print Using mart Ss n mart displayName ds client service getDatasets marl name 0 O print Using dataset ss n ds displayName attr ocllent sServace getAttribures ds name None None l0 O print Using attribute Ss n attr displayName query lt DOCTYPE Query Query client pythonclient processor N TSVN limit 10 header 1 gt lt Dataset name 3s config s gt Attribute name s lt Dataset gt lt Query gt ds name mart name attr name print Query is query results client service getResults query print Results are n results Execute the Python script to see the output python biomartclient py bios smart 78 11 5 Semantic Web API The Semantic Web API is available through a REST interface Interactions with the API are carried out through access points as they are defined in MartConfigurator The access point that is addressed is always part of the URL when using the REST interface Two operations are supported by the Semantic Web API 1 Retrieval of meta data 2 Querying of data Meta data of a mart is available on an access point basis which allows the retrieval of the datasets attributes and filters that are linked to the given access point The meta data is presented in form of an ontology Ontologies can be automatically generated using MartConfigurator and they can be viewed using OWL Tools as de
13. ES n defaut B report BI da Add Access Point v Show hidden c Name Description Source msd_config The User Management window will appear showing the current user group and users 6 0 User Management group anonymous location P 8 user anonymous openiD openID The upper left panel shows the existing user groups and the lower left panel shows the users in the currently selected group By default there is one user group containing one user both called anonymous This user group is used for users who are not logged in bios smart 40 To add user groups click the button underneath the group panel 3 06 group anonymous location 1 user janonymous openiD openID You will be prompted to enter a group name After entering a name your user group should appear in the list of groups and a user of the same name will appear in the list of users To add a user to a user group select the group in the upper panel by clicking its name then click the button underneath the user panel and enter a name for the new user when prompted To allow the user to login you must enter openID credentials in the lower left corner Ke group anonymous secure location user example e openiD openlD http foo myopenid com biossgsmart 41 This allows remote authentication Currently Gmail addresses
14. Start Server button on the top right corner to quickly launch BioMart web server This will also open up your web browser and navigate to BioMart server at http localhost 9000 Please be patient it takes few moments before the BioMart server starts Alternatively to deploy BioMart from command line from the directory of your installation run the following command Jdist scripts biomart server sh start To stop the server please do Jdist scripts biomart server sh stop It may take several minutes before the server starts up and the site is viewable Once server started please navigate your browser to the proper host and port you just set up e g http localhost 9000 biossgsmart 44 7 Configure Deployment You can also deploy BioMart server from the command line on a server In a text editor open the biomart properties file located in the dist subdirectory of the BioMart installation directory In the HTTP settings section change the http host property to 0 0 0 0 and change the http port property to the port on which you would like the non secure web server to run default 9000 Remove 7 at the beginning of http url line and set it to the public URL port from where your BioMart server is accessible for example http url http your domain org 9000 In the BioMart Applications Settings section change the biomart registry file property file to point to yourfilename xml instead of default xml
15. a lists of Datasets that can be linked with the Dataset s specified Method getLinkables Parameters 9 Nonnull String datasets Comma separated string of datasets Returns List lt org biomart api lite Dataset gt bios smart 88 11 6 2 Query The org biomart api Query object provides methods to build and execute a query Note The Query object s methods return the object itself This allows for method chaining 11 6 2 1 Set Processor Method setProcessor Parameters Nonnull String processor Sets the processor that the query engine will run through Default is TSV Returns org biomart api Query 11 6 2 2 Set Limit Method setLimit Parameters int limit The number of result rows to be printed Returns org biomart api Query 11 6 2 3 Enable Header Method setHeader Parameters boolean header If true the results will include a header as the first row Default is true Returns org biomart api Query bios smart 89 11 6 2 4 Set Client Name Method setClient Parameters 0 Nonnull String client The name of the client executing the query You can choose a name that includes your organization Default is biomartclient Returns org biomart api Query 11 6 2 5 Add Dataset This method returns a org biomart api Query Dataset object that will allow you to add Filters and Attributes Method addDataset Parameters Nonnull String name The name of the Dataset Nullable String con
16. 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 biossgsmart 25 L Import from sources 7 Search la omm gt root internalname displayname alse 0c7 datasethidevalue master readonly 9 assword s zs lt Lo Lo e a IS m CH nm o o 3 3 The top half of the window shows a tree view of the objects in the config Containers can be expanded or collapsed by clicking on the triangle next to its name The bottom half of the window shows various properties of the highlighted object and their values biossgsmart 26 The display name of any object a container attribute or filter can be changed by selecting that object by clicking on it and then double clicking the displayname property in the lower right hand pane L gt import from sources Search id v 9 msd config v Di root v t3 ATTRIBUTES v Features H MSD ENTRY DATA 8 MSD ASSEMBLY DATA H3 MSD CHAIN DATA H3 EXTERNAL IDENTIFIERS 8 HETGROUP 8 JOURNAL gt F gt 5 FILTERS Value entry SD ENTRY DATA maxcontainers maxattributes biossgsmart 27 Any object can be hidden from the end user by right clicking on that object and selecting Hide from the menu OO Import from sources Search ll v 9 msd config v root v iH ATTRIBUTES v iH Features v E MSD ENTRY DATA Co
17. are supported as are openID URLs which may be obtained free of charge via www myopenid com Once configured users can log in by clicking on the link at the top of the deployment website Similarly to remove a user or group select it by clicking on its name and then press the button beneath the user or group panel biossgsmart 42 5 14 Hiding an access point The current user group is shown and can be changed at the top of the Portal panel H Portal a de Add Access Point v Show hidden c Name Description Source E msd_config To hide a config from users of the current user group select the access poing right click on the access point icon and unselect Activate such that there is no longer a checkmark next to it The access point parent GUltab can be inactivated in a similar manner in its right click menu and visibility changes to access points under a GUltab cannot be made unless the tab is active default W da Add Access Point v Sh Name Description msd_config Edit Rename Remove Cut Copy Paste Properties Generate Semantics v Activate Hide Readonly Set Group The green C icon will turn grey to indicate that it is inactive for this user group NOTE this only changes the visibility for the current user group Visibility for each user group must be set independently bios smart 43 6 Deploy BioMart WebServer After all the changes have been made you can click the
18. file property file to point to the xml file generated in section 10 1 1 Change the biomart registry key file to point to the key file generated in section 10 1 1 note that it begins with a period You may biossgsmart 61 need to copy these files from the machine where you configured to the server on which you intend to deploy if the two they are not the same machine Save your changes to the properties file before launching the Server To start the server from your BioMart install directory run the following command Jdist scripts biomart server sh start It may take several minutes before the server starts and the site is viewable To stop the server enter Jdist scripts biomart server sh stop biossgsmart 62 11 BioMart API The BioMart API Consists of three parts REST API SOAP API and Java API All three APIs have access to the same methods so you can choose the one you are most comfortable with 11 1 Query XML The XML s root element must be lt Query gt and must specify these attributes client name of the client making the call choose something appropriate e formatter any valid processor name e g TSV CSV HTML e limit the number of rows to return 1 for no limit header if set to 1 then first row of results will be column headers The lt Query gt element can contain one or more lt Dataset gt elements with the following attributes e name the name of the dataset e accesspoint opt
19. new plugin create a new file guitype properties under dist plugins myplugins with the properties displayname and url The content should look as follows displayname My Plugin url myplugin This will create a new GUI type with name myplugin displayName My Plugin and URL myplugin Note The URL must match the directory name of the plugin Note The URL can include up to two s strings When assigned to a GUI container and viewed through the landing page the first s is replaced with the GUI container s name and the second s is replaced with the MartConfig s name if applicable You may need this information for your plugin e g myplugin gui s amp mart s You should now have the basic plugin structure ready for deployment dist plugins myplugin guitype properties public myplugin index jsp 9 2 Using the new plugin To see your plugin in action simply deploy the server as normal from the biomart java directory or from MartConfigurator s Start Server button Jdist scripts biomart server sh start bios smart 51 Once the server has started you can see your new plugin in action by viewing the URL http Aocalhost 9000 myplugin o b P L2 WP _ WP n X ms gt gt GO GO sik Most Visited System Dashboard floalines 28264 un Employee guide BuildBot BioMart Stack Overflow BioMart MartView ReG4S Bookmarks S Qi Recently Bookmarked e R by exampre urr
20. processors and create your processor class inside The processor class has to implement the public void printResults QueryRunner qr OutputStream outputHandle method At minimum you will need to set the output handler of the QueryRunner instance For example the TSV processor simply sets the outputHandle from the method s argument as the output handle of the QueryRunner instance TSV java package org biomart processors import java io IOException import java io OutputStream import java sqi SQLException import org biomart common exceptions TechnicalException import org biomart queryEngine QueryRunner public class TSV implements ProcessorInterface Override public void printResults QueryRunner qr OutputStream outputHandle throws TechnicalException SQLException IOException OR setOutputHandle outputHandle DEAN OR runQuery catch InterruptedException ex 2 j The default output format is TSV columns separated by tabs rows separated by newline characters In order to change the output format you will need to either implement your own java io OutputStream that extends java io FilteredOutputStream or wait until all results come back from the outputHandle and post process it before writing to the output handle of the QueryRunner instance bios smart 57 When you are finished with the implementation use the IDE to build your project to a JAR file Create a directory under plugins that hol
21. results txt Default is false Returns The result returned from the Query XML 11 3 5 Simple Example The following is an introduction to how the REST API may be used to retrieve data We will use the curl program in command line It is assumed you are accessing the server at http localhost 9000 If this is not the case please change the corresponding URLs Retrieve list of Marts curl http localhost 9000 martservice marts Remember one of the Mart s name and config e g name hsapiens gene vega config config hsapians gene vega config Retrieve list of Datasets from the Mart curl http localhost 9000 martservice datasets mart hsapiens gene veg a config Hemember one of the Dataset s name e g hsapiens gene vega Retrieve list of Attributes from the Datasets and config bios smart 15 CULL http localhost 9000 martservice attributes datasets hsapiens ge ne vega amp confrgshs piens gene vega conrig Hemember one of the Attribute s name e g vega gene id Build your Query XML and save it to a file query txt query DOCTYPE Query Query client 2 biomartclient processor TSV limit 2 1 header 1 gt lt Dataset name hsapiens gene vega conflg hsapiens gene vega coniig Attribute name vega gene id Dataset Query Call the results method to get the data curl d guery txt http localhost 9000 martservice results You should see the results printed on your terminal
22. the top of the screen depending on your system allows you to create a new registry open an existing registry or save the registry that is currently being worked on Saving a registry for the first time automatically encrypts any passwords and generates a key file needed to decrypt it The key file name is given based on this convention it starts with a period followed by the registry file name with xml being removed For example key file name will be myregistry when the name of the registry file is myregistry xml Using the Save as option to rename a file will also generate a new key file The key file with a proper key is needed to decrypt all passwords the next time the registry is opened with MartConfigurator or is used to deploy a BioMart server The Source panel A contains a list of dataset sources that are in this registry You can add a new data source by clicking on Aad Source B The Portal panel contains information about the configurations configs in the registry The controls in the Portal tab will be inactive until a data source biossgsmart 12 is added to the registry The visibility of each config can be set differently for different user groups The active user group whose visibility settings are displayed and configurable is shown in drop down C Access points are organized into GUltabs which determine how they are presented to the user The current GUltabs are listed in E and a new GUltab
23. valuelc value2c value3c JSON Returns a JSON object containing the results and the total number of rows found Note The results are not streamed to the client when using the JSON processor This means that data will be written only when the entire result set is ready which may not be ideal for slower queries Example total EE data f Attributel valuela Attribute2 value2a Attribute3 value3a bios smart 64 Attributel valuelb Attribute2 value2b Attribute3 value3b by Attributel valuelc Attribute2 value2c Attribute3 value3c 11 3 REST API The REST API is built on top of hte Java API for RESTful access This API supports two response formats XML and JSON Both formats return the same data in different serialized representations The following are two different representations of the same Mart XML Representation Default mart description gene vega config displayName gene vega config name gene vega config config gene vega config isHidden 2 false meta operation MULTISELECT gt JSON Representation isHidden false displayName gene vega config conrag i gene vega Conrig operation MUBLTISELBECT meta name gene vega config description gene vega GOnlig 11 3 1 Specifying Response Format There are two ways to specify the response format Adding the corresponding HTTP Accep
24. 000 myplugin gui default amp mart gene nj Ga Recently Bookmarked e R by example Grilled Tamarind Sal How Much Is Enough Welcome to Solr Federated search usi RFCAIR o Disable Cookies p CSS 7 e Forms v Images v w Information LX Miscellaneous a Outline BR Resize 7 w Tools it l Ze Disable My Plugin T My Plugin Selected GUI Container GUI default Number of marts 2 Selected Mart Mart gene Operation MULTISELECT E E gt BER v 911 SENSED Me SIOW x L A The JavaScript make a MartService API call to fetch the GUI container information This example demonstrates how to interactive with the MartService API within your plugin 9 4 Custom Processors server side component A plugin may include one or more custom processors A processor is used to return query results in different formats By default BioMart comes with the TSV tab separated value processor To create a new processor you will need to create a new Java class in the org biomart processors package that implements bios smart 56 ProcessorInterface in the same package The name of the new processor class is the same name that is used in the Query XML The easiest way to create this class is using a Java IDE such as Eclipse NetBeans or IntelliJ In the IDE create a new Java project and add the biomart 0 8 jar file from the dist lib directory to the project s Library Add a new package named org biomart
25. 1 0 st v2 mwwith affy hugene 1 0 st v1 wwwith affy hugenefl Classes EA E Object Properties Data Properties Individuals OWLViz DL Query OntoCGraf Usage n u Uwn ws n M Qrg Annotations Characteristics DES Functional Description Domains intersection Ranges Equivalent properties Super properties Disjoint properties D ES ud s No Reasoner set Select a reasoner from the Reasoner menu Class Dependencies in Protege Showing Dataset Usage bios eMart M Show Inferences 82 A O ontology http 10 0 3 31 9000 martsemantics my access point ontology http localhost 9000 martsemantics my access point ontology er ontology htt BDO Active Ontology Entities Classes Object Properties Data Properties Individuals OWLViz DL Query Class hierarchy Dataset OntoGraf Dee lat GA contains Sa Search J Clear v Thing Dataset hsapiens_gene_ensembl my_access_point ti ao fs ABS MRS LALOTA amp JG ot my access point hsapiens gene e nsembl Ms EE SCH D hsapiens gene e nsembl No Reasoner set Select a reasoner from the Reasoner menu v Show Inferences 11 5 2 Semantic Querying Using SPARQL SPARQL queries can be gene
26. 4 MartWizard Datasets Filters Output Restart lt Prev FEATURES MSD ENTRY DATA M PDB ID s O Experiment Type O Authors O Submission Date O Resolution R Work MSD ASSEMBLY DATA O Assembly Type 5 12 5 A m root 4 ATTRIBUTES d lig Features MSD ENTRY DATA L MSD ASSEMBLY DATA L MSD CHAIN DATA EXTERNAL IDENTIFIERS HETGROUP i JOURNAL O Title O Header O Keywords O Release Date LJ Space Group O Assembly Code MartExplorer Datasets Filters Output Restart Prev rer MSD ENTRY DATA M PDB ID s O Experiment Type O Authors O Submission Date CJ Resolution R Work bios O Title O Header O Keywords O Release Date CJ Space Group IEN SUMMARY view xml Database msd config Datasets MSD protein structures Filters Experiment type Fibre diffraction electron e Attributes PDB ID s e SUMMARY view xml Database msd config Datasets MSD protein structures Filters Experiment type Fibre diffraction electron Attributes PDB ID s 39 5 13 User management BioMart supports multi user access such that configs can be individually set to be visible or hidden for different groups of users To manage users and user groups click on the user management icon located to the right of the user group dropdown at the top of the Portal tab User group anonymous
27. 52 _ vega mart 53 vega mart 54 vega mart 55 vega mart 56 _ vega mart 57 vega mart 58 _ vega mart 59 Il f vega mart 60 vega mart 61 e Abort Add Once you have made your selection you will be prompted to use the existing config biossgsmart 16 Add Data Source Type RDBMS gt Name C group Database type MySQL M Using MyISAM Source Schema Relational Mart Host martdb ensembl org Port 5316 Database JDBC URL jdbc mysql martdb ensembl org 5316 y Username anonymous Password Get e Schemas vegd rridrt z vega mart 49 M vega mart 50 C Do you want to use the existing config vega mart 51 f vega mart 52 enee e Cro D mese vega mart 53 f vega mart 54 r f vega mart 55 vega mart 56 vega mart 57 vega mart 58 vega mart 59 vega mart 60 vi vega_mart_61 Select Yes and then click the Add button without changing any other settings to import the configuration from existing mart To add a new data source from a materialized mart and ignore the existing configuration follow the instructions for importing a RDBMS Relational Mart but select No when asked if you want to use the existing config Then select a top level main table eg gene table in Ensembl mart from which to create your new data source and press Add Note that using this method y
28. 66 NR m EMI ee eee ee O ee ne ee eee eee ee ee ee eee 66 We M E 68 NW E GE e E 69 iN H ee CI 70 MT pee EUR MS ERR T T 71 Hs Fe Po E Eet 72 TES 3 7 Linkabie VAC EE 74 oa E e EE 75 TES 351BIDIG eene 75 UE ME I i 76 LLAT ACCESSING SOAP APT U Sie E 76 11 4 2 Accessing SOAP API Using Python uiii tuis ntt trece trarre tee 78 1ko Somanuc Web AP 79 11 5 1 Meta Data Retrieval Working with Ontologies sss 79 11 5 2 Semantic Querying Using SPAR OU ortctinstenottni cendum scimus saine 83 IEO CR a T 85 UN BEE e E V ea E 85 a se Mees ee E 85 NR e ee ERR tee NEE 86 ad CEPR E 86 TOTA E 86 ial Ec it E msc E 87 oS shu KE eg ele dE 87 TLO En E 0 212 0 generar reer eee nee eee eer ee eee eee 88 11 6 1 8 Linkables RE EE 88 EE Ee 89 TLOZ T SL POC E 89 IBERIA ld u M 89 PU Tobe Ee E 89 C T ks S dv 12 11 6 2 4 Set Client NaMe o ccccceccccccccccsssscsscsscsscssesscssccccscssceseuseeceessessceseesecsecsersausseeseusersecsarsneaness 90 11 6 2 5 Add WR EE 90 TILOS ay Da o e E E E ee E 90 Oad AFO aa 90 WG 2 ACAMBI ic eect E E 91 11 6 3 3 Return Query ees seneenresessnrrnesesnrneensnrrnnnsnreennsnrinensnnreeensnrrnenssnreeennnrrnennnnrnnennnnreenn
29. BioMart 0 8 User Manual release candidate 6 May 2011 biossssmart Stee Contents PEGE CUS ICG S t 5 Download BIO M E gd 5 Compile and Build BIOMUALL ccciciiec tior ea hehe eun EO exe on PtI a eee adaa 5 e SUA E 6 USMO Mir Conna OT es 12 od The MartConfigu urator WIBOOW sassosessoessie aaa ia a 12 5 2 Importing data EE 14 S9 Adding anew URL M 14 o Adding anew RDBMS SOUT CO it ptrrtecunici iem rue to dedere era eser haeo cece ices 16 341 Addinganew Relational E dE 16 5 4 2 Adding a new Source Schema Virtual Mart eere 17 5 5 Manipulating a Mart using the Schema Editor sss 20 50 Materializing a Virtual Ma E enses a DRE EID 21 5 7 Adding marts from Registry File eese eee nennt nnne tenter tese nnns 24 5 8 Creating and modifying an access point sse nennen tentent nnns 25 S aei cBadeie E 29 SLO Creating links DebWeeli SOUPOGS EE 31 SE EE 35 5 12 Changing the GUI type for a config sssssssssseseeeneernne nennen tete tnn ntn ntes 36 Dd M e EE 36 5 12 2 MartAnalysis esce tentorio rente oneeiuvacsu ncs tatam s rxvuR pax ienci uostri cunas ico EeE LUE Eta guxa EMEN TUNUS EDEN 37 9 12 3 NISEPEBOEEH E 38 ee IZ D 39 ee MAEDOG eet 39 so cy Ga EE E 40 SA Hidinganacces
30. ID s Title Experiment Type Header 2 Authors 2 Keywords Submission Date 2 Release Date Resolution Space Group R Work gt MSD ASSEMBLY DATA ff MSD CHAIN DATA w Property If no link exists between the sources a Dataset Link Dialog will appear allowing you to create a link DOSis mari 32 ee Dataset Link Dialog v iH Features L v 9 msd config v Di GENE v root gt Hj Vega v DD ATTRIBUTES v EXTERNAL v FEATURES v amp External References gt Hj MSD ENTRY DATA Com gt amp 3 MSD ASSEMBLY DATA 9 CCDSID v E MSD CHAIN DATA 2 Ensembl Human Gene 2 UniProt ID s ENST CDS ID 2 Chain code 2 ENST Identical ID 2 Chain length 2 HGNC ID EBI Chain Code 9 HGNC symbol 2 Molecule code 2 IMGT HLA 2 Molecule name 2 IMGT Gene 2 Molecule ID 2 Pubmed ID 2 Molecule src method 2 Tax concat Scop concat Cath concat 9 RefSeq DNA ID 2 RefSeq predicted DNA ID 9 RefSeq RNA ID 2 RefSeq predicted RNA ID 9 RefSeq Genomic ID 9 Sws concat 2 EntrezGene ID gt 3 JOURNAL MIM Gene ID gt B FILTERS gt DD PROTEIN b Id Crruetureor b Selected attributes in hsapiens_gene_vega Selected attributes in msd_config UniProt SwissProt Accession UniProt Accession ID s y SS o Cancel OK ee ee Select the attribute s on which to base the link in both sides by double clicking Multiple attributes can be selected to for
31. _snp amp config snp_config Sample XML Response lt filters gt lt filter isHidden false qualifier type singleSelect description displayName Chromosome name name chr name gt value isSelected false displayName 1 name 1 gt zen ELEME Sample JSON Response Name Chr name displayName Chromosome name description ve type singleSelect isHidden false bios smart 70 qualifier Y v Itrilters s T values f isSelected false names 13 displayName 15 by 11 3 3 5 Attributes Lists all the attributes for the given Dataset s URL martservice attributes Method GET Parameters datasets required Comma separated string of Datasets config optional The name of the config as returned by the Mart object You should provide this when the Mart s config is non empty container optional The name of the container you want to return attributes for Returns List of attribute objects Sample URL martservice attributes datasets btaurus snp amp config snp config Sample XML Response attributes lt attribute isHidden false linkURL species2 Variation Summary v s value description _displayName Variation ID name refsnp id gt lt fJatcribures gt bios smart 71 Sample JSON Response name refsnp id displayName Variation ID description s mm isHidden false linkURL species2
32. able is org biomart api factory XmlMartRegistryFactory which reads the registry in XML format You do not need to interact with the MartRegistryFactory instance directly as you will see later on 11 6 1 1 Portal The org biomart api Portal object takes in an instance of MartRegistryFactory and provides public methods for access registry information The following are the methods available from the Portal object Note bios smart 85 Parameters annotated with Nullable is an optional parameter and should be passed as null if not used Parameters annotated with Nonnull are required and must not be null or an empty string 11 6 1 2 Root GUI Container Returns the root GUI Container Method getRootGuiContainer Parameters Nullable String type Restricts returning GUI Containers to this type e g martform Returns org biomart api lite GuiContainer 11 6 1 3 Marts Returns a list of Marts Method getMarts Parameters Nullable String guiContainerName Restricts the returned Marts to the specified GUI Container Returns List lt org biomart api lite Mart gt 11 6 1 4 Datasets Returns a list of Datasets Method getDatasets Parameters Nullable String mart The name of the Mart to return datasets from Returns bios smart 86 List lt org biomart api lite Dataset gt 11 6 1 5 Filters Returns a list of Filters Method getFilters Parameters Nonnull String datasets Comma separated string
33. and MartConfig to the end of the URL Change the content of guitype properties to the following displayname My Plugin url myplugin gui s amp mart s 9 3 2 Modify index jsp We will include the jQuery http jquery com JavaScript library in order to access some helper methods Change the content of index jsp to the following biossgsmart 53 lt doctype html gt lt page language java gt 8 page contentType text html charset UTF 8 gt html lang en gt lt head gt lt title gt My Plugin lt title gt lt link type text css href styles css rel stylesheet gt lt head gt lt body gt lt hl gt My Plugin lt hli gt lt div id gui gt lt h2 gt Selected GUI Container lt h2 gt lt div gt lt div id mart gt lt h2 gt Selected Mart lt h2 gt lt div gt lt script type text javascript eroe qTe 115 j 008fy9 1 1 2 l10 8 gt lt 7 Script lt script type text javascript src script js gt lt script gt lt SCript S initialize lt script gt lt body gt lt html gt Note that initialize will call the initialize function which will be defined later when the DOM is ready 9 3 3 New stylesheet Create a CSS stylesheet styles css with the following content body font family Arial sans serif lont saze 12px background color eee margin 10px hl font size 24px h2 color 3555 gui mart border lpx dotted 999 background color
34. can be added by pressing the sign at the right side of the tab bar Initially there are two GUltabs default and report The report GUltab allows creation of report pages Within a GUltab configs can be added by pressing the button labeled Add Access Point D The current registry can be deployed locally for testing using the Start Server button F biossgsmart 13 5 2 Importing data sources There are three types of data sources that can be imported into MartConfigurator URL RDBMS Relational Mart or Source Schema aka Virtual Mart and data sources configured in a Registry File For all of them start by clicking the Add source button C 5 3 Adding a new URL Mart By default the import type is set to URL To import from URL enter your connection parameters and click the Get button in the upper right A list of marts available on the server should then appear in the left panel AOO Add Data Source Type URL ES Name E group Host http www biomart org Port 80 Path biomart martservice Marts Datasets Selecting a Mart in the left panel will show a list of the datasets in this Mart By default all datasets will be checked Clicking on an individual dataset will toggle whether or not it is checked bios smart 14 Type Name 7 group Host http www biomart org Port 80 Path biomart martservice user password key o Datasets C bacterial mart 8 f bacterial seq
35. ddd margin 10px padding Spx 9 3 4 New JavaScript file Now create a JavaScript file script js with the following content bios smart 54 function nitiadlize 1 var queryString location search substr 1 parts queryString split amp Gui partslUl spllit e srhls hart parts ll split l1 gt sa jax 4 url rest json guil gui success unction Jjson var gui json mart for var i 0 mart gui marts i itt if mart name mart break j j S gui append p strong GUI strong gui displayName lt p gt append p strong Number of marts lt strong gt quidiarts length lt p gt S smart append p strong Mart strong mart displayName lt p gt append lt p gt lt strong gt Operation lt strong gt mart opersbtion x p gt The updated directory structure would look like this dist plugins myplugin guitype properties public myplugin index jsp script js styles css bios smart 55 9 3 5 Redeploy Restart the server so it can pick up the new URL structure Jdist scripts biomart server sh restart Now a link to the plugin page should look similarly to the screenshot below CHE Lal amp wv Most Visited System Dashboard Bloglines 28264 un Employee guide BuildBot BioMart Stack Overflow BioMart MartView Re A nj Ri Si http localhost 9
36. ds a single directory called lib Copy your project s JAR file to this lib directory and BioMart will install it automatically Please see the CSV comma separated value processor included in the BioMart SVN repo plugins csvprocessor The source file included CSV java shows an example where a custom OutputStream is created biossgsmart o8 10 Preconfigured Portal Deployment 10 1 ICGC 10 1 1 Changing connection parameters For a local deployment of ICGC you will want to point the configuration to your local database To simplify the update process a new command line update tool is developed To update the included icgc5 xml with your connection parameters you must first create a configuration file that includes those connection parameters Copy and paste the following text to a text file making the appropriate changes to the connection parameters to point to your database i e YOURSERVER becomes your database server address YOURDBNAME is where the ICGC data is loaded to by martloader tool contact ICGC DCC at dcc support amp lists oicr on ca for your DATASETNAME etc config oauth openid https me yahoo com a lyINRct235wrOllONtQMUcKwenvgzlUqbyaA datasets dataset name DATASETNAME database YOURDBNAME dbhost YOURSERVER dbport YOURPORT dbuserz YOURUSER password YOURPASSWORD gt lt datasets gt lt config gt Save this file as update xml in the dist subdirectory of your BioMart in
37. e root Containers name Snpsatts displayName Variation Information description NULL maxContainers O0 maxAttributes O0 independent false attributes hane reisnp zd displayName Variation ID description i M isHidden false IankURL s kspecies2 Variation Summary v s Value Mu attributes IIlLters s T J Containers by biossssmart 73 11 3 3 7 Linkable Datasets Lists all the Datasets that can be linked with the selected Dataset s URL martservice linkables Method GET Parameters datasets required Comma separated string of Datasets Returns List of Dataset objects Sample URL martservice linkables datasets btaurus snp Sample XML Response datasets sSdataset isHidden ralse descraiptron hsaprens snp som displayName Homo sapiens Somatic Variation COSMIC SUP name hsapiens snp som Jdatasets Sample JSON Response isHidden false name hsapiens snp som displayName Homo sapiens Somatic Variation COSMIC SUT description heaprens snp som by bios smart 74 11 3 4 Querying To retrieve data from the REST API you will need to create a Query XML URL martservice results Method GET or POST Parameters query required The Query XML download optional If true then the HTTP response will include the header Content Disposition attachment filename
38. e 27 2008 If you do not have Ant installed on your system you will see a command not found error To install the latest version of Ant please visit the website http ant apache org 12 1 2 Windows users Open up the Command Prompt and type in the commands below following the great than character gt 1 Check for the correct Java version BioMart requires Java 6 1 6 x First check if the JAVA HOME environment variable is set bios smart 94 C gt echo JAVA_HOME C Program Files Java jdk1 6 0_22 If you see a path printed out please follow a otherwise follow b a Check the Java version specified in by JAVA HOME C JAVA_HOME bin java version java version 1 6 0 22 Java TM SE Runtime Environment build 1 6 0 22 b04 307 10M3261 Java HotSpot TM 64 Bit Server VM build 17 1 b03 307 mixed mode b Check the Java version of the java command C gt java version java version l 6 0 22 Java TM SE Runtime Environment build 1 6 0 22 b04 307 10M3261 Java HotSpot TM 64 Bit Server VM build 17 1 b03 307 mixed mode The Java version printed from steps a or b should be 1 6 x if you see 1 4 x or 1 5 x then please update your system to use Java 6 2 Check the ant version number BioMart requires Apache Ant 1 7 or higher C 5 ant version Apache Ant TM version 1 8 2 compiled on December 20 2010 If you do not have Ant installed on your system you will see an error message stating that
39. e replace the URL with the correct address when following this section 9 1 Creating a new plugin Create a new directory under the plugins directory to hold your plugin files cd plugins amp amp mkdir myplugin cd myplugin Your plugin can host new front end files to be exposed by the server Additionally you can create new GUI types to allow the plugin to be assigned to a GUI container 9 1 1 Front end files client side component Create a new directory called public mkdir p public myplugin amp amp cd public myplugin Any files in this directory will be automatically picked up by the BioMart server and can be accessed through a browser under the URL http localhost 9000 myplugin Let s take a basic Hello World approach and create an index jsp file under the public folder with the following content lt doctype html gt lt page language java gt 8 page contentType text html charset UTF 8 gt lt doctype html gt html lang en gt lt head gt lt title gt Hello World lt title gt lt head gt lt body gt lt hl gt Hello World lt h1 gt lt body gt lt html gt You can also just use a plain index html file but we will use a JSP file so we biossgsmart 50 can extend it later with more functionality Note You can also put images CSS and JavaScript files in the public folder For the sake of simplicity we will omit them 9 1 2 Configure To let BioMart know about the
40. ect and selecting hide This will effectively remove that table column or relation from the BioMart representation of the database It can be undone by right clicking the object again and selecting unhide Relations can also be changed between 1 1 and 1 M which will have an effect on how source tables are materialized The Schema Editor window for virtual marts comprises two tabs source and target By default source is selected This shows the tables as they exist in the underlying source database The target tab shows the tables that will be created by materializing Changes made in the source view such as hiding tables and columns or changing relation type will be reflected immediately in the target view In the target view right clicking on a table and selecting Explain Table will show the series of joins that is performed to transform the source schema to the materialized schema bios smart 20 5 6 Materializing a Virtual Mart Materializing a virtual mart considerably improves querying speed for large databases To do this you must first add a virtual mart to your data sources as described in the previous section First you must have MartRunner running From the directory in which you installed BioMart run the following command Jdist scripts martrunner sh 9005 Where 9005 is a port that is free on your machine Next in the MartConfigurator window right click on the virtual mart and select Materialize from the drop dow
41. er import org biomart api lite Mart public class PortalExample public static void ma in Strino args i MartRegistryFactory factory new XmlMartRegistryFactory Users jhsu main xml Portal portal new Portal factory List Mart marts portal getMarts null Soysrtem out praintln 5trring tormat Got 795 marts marts size List Dataset datasets portal getDatasets marts get 0 getName Syvsrem out prrintlin String tormat Got 5S datasets datasets size List lt Filter gt filters portal getFilters datasets get 0 getName marts get 0 getConfigName null ovshtem oHt println Sbtring rtormat Gor 5 filters filters size List Attribute attributes portal getAttributes datasets get 0 getName marts get 0 getConfigName null System out println String format Got Sa attributes attributes size System exit 0 Compile the code and run it javac cp PortalExample java java cp PortalExample biossssmart 92 11 6 4 2 Querying The following is a runnable Java class that demonstrates how query execution can be done QueryExample java import org brolmart dDpil Portal import org biomart api Query import org biomarrt api tactory MarthegistryFactory import org bzromarr apri ractory XmlMarthBegristryPFactory public class QueryExample public static void main String args MartRegistryFactory factory new XmlMartRegistryFactory
42. fig The config of the Mart Please specify this if it is non empty Returns org biomart api Query Dataset 11 6 3 Query Dataset The org biomart api Query Dataset object contains the Filters and Attributes in a Query Note The Dataset Query object s methods return the object itself This allows for method chaining 11 6 3 1 Add Filter Method bios smart 90 addFilter Parameters Nonnull String name The name of the Filter 9 Nonnull String value The value of the Filter Returns org biomart api Query Dataset 11 6 3 2 Add Attribute Method addAttribute Parameters Nonnull String name The name of the Attribute Returns org biomart api Query Dataset 11 6 3 3 Return Query This method return the original Query object that created the Dataset Method end Parameters none Returns org biomart api Query 11 6 4 Simple Example To use the example below make sure the biomart 0 8 jar file and all other dependencies are on the classpath bios smart 91 11 6 4 1 Portal Access The following is a runnable Java class that demonstrates how interaction with the local registry can be done PortalExample java import Jjava util Lbist import org bilomasrt abrforctral import org biomart api factory MartRegistryFactory import org bromarrt apri ractory XmlMartRhBegristryPFactory import org biomart api lite Attribute import org biomart api lite Dataset import org biomart api lite Filt
43. hange the http port property to the port on which you would like the non secure web server to run default 9000 Remove 7 at the beginning of http url line and set it to the public URL port from where your BioMart server is accessible for example http url http your domain org 9000 In the BioMart settings section change the biomart registry file property to point to quickstart xml Change the biomart registry key file property to point to quickstart Note Make sure that the full path to these files is correct based on where you saved them By default this will be in the registry subdirectory of the directory where you installed BioMart To deploy BioMart from the directory of your installation run the following command Jdist scripts biomart server sh start To stop the server use the command Jdist scripts biomart server sh stop lt may take several minutes before the server starts and the site is viewable biossgsmart 10 Once the server is started please navigate your browser to the proper host and port you just set up e g http your domain org 9000 biossgsmart 11 5 Using MartConfigurator 5 1 The MartConfigurator window On first starting up the MartConfigurator window will look like this A B C D E Tl MartCorffigurator Versiorg0 8 demo xml 3 MSD Protein Structures msd MSD Protein Structures The File menu either at the top of the window or
44. in the left panel Click on msd to select and check it Type URL Name H group Host http www biomart org Port 80 Path biomart martservice user password Datasets C bacterial mart 8 l bacterial sequence mart 8 C fungal mart 8 L fungal sequence mart 8 metazoa genomic features mart 8 f metazoa mart 8 metazoa sequence mart 8 C plant mart 8 f plant sequence mart 8 C protist mart 8 f protist sequence mart 8 i msd O htgt C REACTOME C WS220 testing The msd dataset will appear in the right hand panel and will be checked Click the Add button at the bottom of the window to add the data sources The new data sources will appear in the left hand panel on the MartConfigurator window biossssmart 7 V defaut O P Add Source fJ MSD Protein Structures In the right hand panel click the Add Access Point button ANA MartConfigurator Version 0 8 untitled xml E Portal Wdemk I User group anonymous 1 Bi O start server i a sp Add Source l default D report u 4 MSD Protein Structures M Show hidden configs M List View Description Source Group You will be prompted to choose a main data source Click on MSD protein structures and click OK When prompted to choose a name click OK to use the default A new access point will be created and shown in the right hand panel bios smart 8 MartConfigurator Ver
45. ional the accesspoint of the mart if applicable Each lt Dataset gt element may contain zero or many lt Filter gt elements e name name of filter value value of filter Each Dataset element must contain at least one lt Aitribute gt element e name name of attribute Sample Query XML Query client formatter TSV limit 1000 header 1 gt Dataset name hsapiens gene ensembl hopkinsbreasto acgcessposxnre hsaparens gene Snsempl Filter name biotype value miRNA Attribute name ensembl gene id Attribute name cancertype gt Attribute name description gt Attribute name start position Attribute name end position gt lt Dataset gt lt Query gt 11 2 Formatter By default results from a Query are returned in TSV tab separated format To change the format simply change the processor type in the Query XML The following core formatters are available in BioMart bios smart 63 TSV Returns tabular data with attributes separated by a tab character and rows separated by a newline character Example Attributel Attribute2 Attribute valuela value2a value3a valuelb value2b value3b valuelc value2c value3c CSV Returns tabular data with attributes separated by a comma and wrapped around double quotes and rows separated by a newline character Example Attributel Attribute2 Attribute3 valuela value2a value3a valuelb value2b value3b
46. l protect your site with the username martuser and the password 123456 To change the username and or password edit the file realm properties in the dist web etc subdirectory Change the value martuser to whatever username you would like and the value 123456 to whatever password you would like You can also add additional users by adding new lines to the file in the format username password user Note that the user at the end of the line is mandatory For deployment servers you MUST change the martadmin password in the realm properties file To enable HTTPS protocol so that communication between your server and all clients is encrypted please see section 8 1 10 1 6 Advanced deployment For a more configurable deployment e g to set the port for your server you must deploy the server from the command line To do so you must edit the biomart properties file located in the dist subdirectory of the BioMart installation directory In the HTTP settings section change the http host property to 0 0 0 0 and change the http port property to the port on which you would like the non secure web server to run default 9000 for production server use port 80 Remove 7 at the beginning of http url line and set it to the public URL port from where your BioMart server is accessible for example http url http your domain org 9000 In the BioMart Applications Settings section change the biomart registry
47. llation directory and change the property theme from default to your theme of choice theme icgc5 After performing the BioMart build the dist web includes subdirectory of your BioMart installation directory will contain a file header html that you are encouraged to edit to include site logos etc specific to your institution To maintain a consistent look and feel across ICGC portal installations users should avoid making unnecessary modifications to any other files included in the ICGC theme directory 10 1 4 Configuring the location dropdown To enable the locations dropdown on the homepage and add your site you must open the file locations properties in the dist web etc subdirectory of your BioMart installation directory In that file add the line location code yourcode Where yourcode is replaced with your three digit ICGC institution code Contact dcc support lists oicr on ca if you are an ICGC member and do not know your institution code 10 1 5 Security To password protect your entire site while testing you must first edit the file web xml located in the dist web webapps martapps WEB INF subdirectory of your BioMart installation directory Find the line that reads bios smart 60 lt l Uncomment to enable site wide BASIC authentication Line number 14 and delete this entire line Ten lines later there is a line that reads gt Delete this line as well and save the file By default this wil
48. m the link but they must have the same number on each side Lines are shown between to two lists of attributes to show which are being matched Click OK to create the link To see all the links for a source right click on the name of the source in the Source panel and select Link Info 8 0 0 File P Add Source MSD protein structuv777 Dataset Source Management d Danio rerio genes i Update Mus musculus geng ELE Link Index Remove Rename f3 Homo sapiens gene Schema Editor Materialize Query Source Schema bios smart 33 The Link Management Dialog window will appear where you can see to which sources the selected source links Clicking on a link name will then show information about this link in the lower panels ANJO Link Management Dialog Data source MSD protein structures HH v MSD protein structures v F3 Mus musculus genes NCBIM37 _ amp msd mmusculus gene vega link v L3 Homo sapiens genes GRCh37 p2 MSD protein structures gt Homo sapiens genes GRCh37 p2 Homo sapiens genes GRCh37 p2 gt MSD protein structures Attribute Value Attribute Value name msd hsapiens gene vega link name hsapiens gene vega msd link internalname internalname hsapiens gene vega msd link displayname displayname hsapiens gene vega msd link description description hsapiens gene vega msd link pointedmart pointedmart msd pointedconfig pointedconfig msd attributes attributes UniProt Swiss
49. n menu ANDO File H Source WY default 3 transcript Dataset Source Management Update Link Info Link Index Remove Rename Schema Editor Materialize v Query Source Schema The Generate SQL window will appear with all of the text fields blank These must be filled in with the correct connection parameters biossgsmart 21 EN Generate SQL Schema partitions Target database your db Target schema your schema Send SQL to MartRunner 4 MartRunner host name localhost MartRunner port number 9005 Database server name your db server Database server port number 3306 Abort Generate SQL The proper information for the Target database and Target schema fields differ depending on the database server type MySQL Target database and target schema must be the same and different than the original source database and schema The database must exist on the server SQL Server Target database and target schema both must exist on the server The original source schema should not be used PostgreSQL Oracle and DB2 Target database must be the same as the original source The target schema should exist within this database and should be different than the original source schema The MartRunner host name is localhost and the MartRunner port number is whatever you chose when executing the martrunner command e g 9005 The Database server name and Database server port number
50. nnrenennnrees 91 IRIS ME EKN UE 91 EO tie Gelle CHE 92 BE CH Lu D 93 Troubleshooting Installation eere 94 Ke SUSPBLODSC ES cured N ere AE E eee 94 TEE lt N 18 SUC e RR 94 TE WAON EE 94 122 TESSU A gene EE 95 biossgsmart A 1 Prerequisites Software Java 1 6 Ant and GIT client OS major Linux distributions Server min one GB memory three GB for better performance 2 Download BioMart From the directory in which you wish to install BioMart run the following command git clone https github com biomart biomart rc6 git 3 Compile and Build BioMart From the directory in which you installed BioMart run the following command ant This will compile BioMart source and build the distribution biossgsmart 5 4 Quick Start This section will show you how to add the MSD protein structures dataset and deploy the BioMart server Run MartConfigurator with the following command in the directory of your installation Jdist scripts martconfigurator sh In the MartConfigurator window click Add a new data source in the upper right corner ADO File In the Add Data Source window that appears click the Get button to connect to BioMart central portal 70 Add Data Source Type URL H group Host http www biomart org Port 80 Path biomart martservice Dassworc Datasets bios smart 6 A list of available marts will appear
51. of Datasets Nullable String contig The name of the config as returned by the Mart object You should provide this when the Mart s config is non empty Nullable String container The name of the container you want to return filters for Returns List lt org biomart api lite Filter gt 11 6 1 6 Attributes Returns a list of Attributes Method getAttributes Parameters Nonnull String datasets Comma separated string of Datasets Nullable String contig The name of the config as returned by the Mart object You should provide this when the Mart s config is non empty Nullable String container The name of the container you want to return attributes for Returns List org biomart api lite Attribute bios smart 87 11 6 1 7 Containers Returns the root Container which containers all subsequent Containers Note Containers and GUI Containers are different objects Method getContainers Parameters 9 Nonnull String datasets Comma separated string of datasets Nullable String config The name of the config as returned by the Mart object You should provide this when the Mart s config is non empty Boolean withattributes If true containers with Attributes or descendent Containers with Attributes will be included Boolean withfilters If true Containers with Filters or descendent Containers with Filters will be included Returns org biomart api lite Container 11 6 1 8 Linkables Datasets Returns
52. ou can only select one dataset at a time 5 4 2 Adding a new Source Schema Virtual Mart Source Schema option in RDBMS type is for importing relational sources based on the 3NF schema by dynamically creating a non materialized virtual mart To add a new virtual mart based on a source schema first add a new data source by clicking on the Add Source button Select RDBMS from the Type dropdown select Source Schema radio button and then select your database type from the Database type dropdown Then fill in the Host Port Database Username and Password parameters to connect to your database server the Database field is optional for MySQL servers The JDBC URL field is populated automatically and should not be modified bios smart 17 0 00 Add Data Source Type RDBMS ES Name D group Database type MySQL HH M Using MyISAM Source Schema Relational Mart Host ensembldb ensembl org Port 5306 Database JDBC URL jdbc mysql ensembldb ensembl org 5306 i b Username anonymous Password Get Schemas Tables homo sapiens vega 49 36k homo sapiens vega 50 36l homo sapiens vega 51 36m homo sapiens vega 52 36n homo sapiens vega 53 360 homo sapiens vega 54 36p homo sapiens vega 55 37 homo sapiens vega 56 37a homo sapiens vega 57 37b homo sapiens vega 58 37c homo sapiens vega 59 37d homo sapiens vega 60 37e homo sapiens vega 61 37f
53. page and a hyperlink will be created on this attribute for linking to the report page Clicking bios smart 29 the Select button will create the new access point Now the report page would appear as hyperlink on the attribute selected e g PDB ID in the Web GUls See example below MSD Protein Structures Displaying results 1 20 out of 1000 Results beyond 1000 are not displayed use the download link to retrieve the complete results H Bookmark XML SPARQL Java Download data E Click on a column heading to sort PDB ID s Assembly Type Molecule Name 11ba DIMERIC RIBONUCLEASE SEMINAL 103d DIMERIC DNA 5 D GP TP GP GP AP AP TP GP GP AP AP C 3 ANTI PARALLEL DNA DUPLEX HUMAN CENTROMERE REPEAT 103 DIMERIC T4 LYSOZYME 104d DIMERIC DNA RNA CHIMERIC HYBRID DUPLEX 5 R CP GP CP G D TP AP TP AP CP GP CP G 3 1041 MONOMERIC LYSOZYME INS S44 AA C54T C97A 107d DIMERIC DNA 5 D CP CP TP TP TP TP C 8 5 D GP AP AP AP AP GP G 3 COMPLEXED WITH DUOCARMYCIN DC88 A A MINOR GROOVE BINDER 108d DIMERIC DNA 5 D CP GP CP TP AP GP CP G 3 10mh NONAMERIC CYTOSINE SPECIFIC METHYLTRANSFERASE HHAI 10mh NONAMERIC DNA 5 D P CP CP AP TP GP CH3 CP GP CP TP GP AP C 3 10mh NONAMERIC DNA 5 D P GP TP CP AP GP 5NCP GP CP AP TP GP G 3 Click on the PDB ID hyper link will bring up the report page as below Home gt report Not logged in Login REPORT PDB ID s llba Go is ATTRIBUTES PDB ID s 11ba 1
54. path to xml Portal portal new Portal factory Query query new Query portal SetProcessor TSV SetClient test SetHeader true SetLimit 10 addbataseti hsapiens gene ensembl hsapiens gene ensembl config Jaddrilter ohromosome name I addAttribute eusembl gene id end query getResults System out System exit 0 Compile the code and run it javac cp QueryExample java java cp QueryExample bioesssmart 93 12 Troubleshooting Installation 12 1 System checks This section will help you determine whether the environment requirements have been met before you continue with the rest of the guide If the system requirements are not met you may need to speak to your system administrator to perform an upgrade 12 1 1 Nix OS X users Open up a Terminal window Type in the commands below following greater than character gt 1 Check the Java version BioMart requires Java 6 1 6 0 gt if JAVA_HOME then JAVA_HOME bin java version else java version fi java version 1 6 0 22 Java TM SE Runtime Environment build 1 6 0 22 b04 307 10M3261 Java HotSpot TM 64 Bit Server VM build 17 1 b03 307 mixed mode The Java version printed should be 1 6 x if you see 1 4 x or 1 5 x then please update your system to use Java 6 2 Check the ant version BioMart requires Apache Ant 1 7 or higher gt ant version Apache Ant version 1 7 1 compiled on Jun
55. prot Accession s e g Q6VEP3 datasets hsapiens gene vega datasets msd biossgsmart 34 5 11 Creating a link index Indices can be created for links in order to speed up searching To do so right click on a data source in the Source panel and select the Link Index option eoo File Source N D V defaut O P Add Source MSD protein struct 7 Dataset Source Management Update L3 Mus musculus gef Link Info J Danio rerio genes fJ Homo sapiens ge Remove Rename Schema Editor Materialize Q J V C t The Link Index window will appear AOA Link Index Link msd hsapiens_gene_vega link r3 indexed msd true To create an index select a link from the Link dropdown at the top of the window Next click on a dataset for which the link is to be created multiple datasets can be selected using the shift key and the click the Create button bios smart 35 5 12 Changing the GUI type for a config All access points within a GUI tab must have the same GUI type in the interface To change this type right click on the GUI tab you want to modify select Set GUI type and choose the GUI type from the list User group anonymous Start Server default mi renort Ml Rename dk Add Config MI Remove M List View Name Description Paste 1 Group 9 msd config msd Properties structu dal Mart Search v Activate v Mart Form Add sub tab Sequence Converter Mart Analysi
56. py Cut Remove Create filter Move up Move down Show all references 2 R Work gt E MSD ASSEMBLY DATA displayname PDB ID s description mer O O biosi mart 28 5 9 Creating a report A report is a specialized type of access point that gives information based on a single attribute key that is used to retrieve information from our main source and other linked sources Note that a report can only be created based on an existing config To create a report click on the report GUltab zi Add Access Point v Show hidden configs v List View Name Description Source Group msd_config msd MSD Protein Structures Then click on the Add Access Point button defaut B report W CE Aaa Access Poine gt Show hidden configs Mi List View Name Description Source Group msd_config msd MSD Protein Structures You will be prompted to choose a main data source You must choose a data source that has at least one existing config if you choose a data source with no config an error message will appear After being prompted to name the new config you will be asked to choose an attribute to serve as the main attribute for the report page O Please select the identifier field for the report Assembly Class Assembly Type Authors Experiment Type Header Keywords PDB ID s Resolution Space Group Cancel IL Select The attribute you select will be used as the key for the report
57. rated using the MartView interface A SPARQL button is shown above the tabular result set for generating a SPARQL query that will return the same result set as shown ij Bookmark REST SOAP 2 SPARQL 2 Java Download data Working with the generated ontology from above the SPARQL button will for example show biossgsmart 83 SPARQL Query rdf lt http www w3 org 1999 02 22 rdf syntax ns gt rdfs lt http www w3 org 2000 01 rdf schema gt owl lt http www w3 org 2002 07 owl gt accesspoint lt http lLocalhost 9000 martsemantics my_access_point ontology gt class biomart localhost 99000 martsemantics my access point ontology class dataset biomart localhost 99000 martsemantics my access point ontology dataset attribute biomart localhost 9000 martsemantics my access point ontology attributes a a1 FROM dataset hsapiens gene ensembl WHERE 1 mart attribute chromosome name X mart attribute with entrezgene only mart attribute ensembl gene id a mart attribute entrezgene a1 This query can be submitted via HTTP GET request For example cur L can be used to make SPARQL queries as follows curl H Accept application spargl resultst xml v http localhost 9000 martsemantics my access point SPARQLXML get query http encoded SPARQL query The result will be returned as SPARQL XML For the example SPARQL query the result looks as follows lt xml version
58. red Tamarind Sal How Much Is Enough Welcome to Solr Federated search usi RFC Disable Cookies Y CSS Forms Images m Information CA Miscellaneous 9 Outline f Resize v bs Tools 3 Hello World Hello World You can assign the plugin to a GUI container through MartConfigurator From the usual Set GUI Type dialog select the new My Plugin type E rename Remove Paste Properties Set GUI Type gt Demo v Activate Mart Search vaft 5earc Add sub tab v My Plugin Mart Form Mart Ana VSIS Mart Explorer Mart Wizard Hestart the server and the links under the GUI container with the new type will have the correct URL i e http Aocalhost 9000 myplugin bios smart Lol C Go Go I Most Visited gt System Dashboard Bloglines 28264 un Employee guide BuildBot BioMart Stack Overflow BioMart MartView ReG amp S el s j Recently Bookmarked e R by example Grilled Tamarind Sal How Much Is Enough Welcome to Solr Federated search usi BECE Disable Cookies xg CSS Forms Images v Information L Miscellaneous Outline RI Resize 7 b Tools Your Site Title Here Home Not logged in Login JEFAUL Dataset summary gene vertebrates EE gene ee Powered by Diossssmart 9 3 An advanced example Go back to the plugins myplugin directory 9 3 1 Change plugin URL We will now append additional information GUI container
59. replacing yourfilename xml with your registry file name Change the biomart registry key file to point to yourfilename instead of default again replacing this with a period followed by your actual registry name without the xml extension To start web server see section 6 biossgsmart 45 8 Security 8 1 Secure web connections HTTPS If you would like secure access to your BioMart deployment you will need to further configure your biomart properties file in the dist subdirectory of the BioMart installation directory Modify the HTTPS settings section as follows In the HTTPS settings section remove the at the beginning of the line for the https port property and change this to the port on which you would like the secure web serve to run default 9043 Later in the HTTPS settings section remove the from the beginning of the lines for ss keystore and ssl password Set the ss password property to a password of your choice This password will be used again later in this process Next you will need to have to a valid SSL certificate for the domain that you plan to use to deploy the BioMart server Here we demonstrate how to generate the self assigned SSL certificate From the root directory of your installation change to the dist web etc directory with the command cd dist web etc If a keystore file exists delete it using the command Generate a new keystore file using the command
60. s GRCh37 p2 D vO hsapiens_gene_vega datasetdisplayname Le Value Qgene vega sapiens gene vega false o DL eS v tB root v ATTRIBUTES v Features v amp MSD ENTRY DATA PDB ID s Title 2 Experiment Type Header Authors 2 Keywords Submission Date Release Date Resolution 2 Space Group R Work gt 3 MSD ASSEMBLY DATA gt MSD CHAIN DATA msg KE IAS DL poc displayname metainfo datasetdisplayname You can change the source using the drop down menu at the top of left panel Once you have selected the desired source in the left panel find the target attribute or filter for the pointer and drag it to the container in the right panel where you want the pointer to be created v 6 root Hide sources 37 Search Ej Source Homo sapiens genes GRCh37 p2 H v Q hsapiens gene vega v amp ATTRIBUTES v Features v amp B GENE v Di Vega e VEGA transcript ID VEGA protein ID Canonical transcript stable ID Description Chromosome Name Gene Start bp Gene End bp Strand Band Transcript Start bp Transcript End bp e Le _ Drag and drot vega_g i Mgagen id A gene ID ega Stable ID of the Gene SSES EE SS false v 9 msd config v Bi root v 8 ATTRIBUTES v amp Features HEET ENTRY pata PDB
61. s Mart Explorer Mart Wizard There are four different GUI types supported in the current release MartAnalysis MartForm MartWizard and MartExplorer Three other GUI types shown above are currently under development These GUls offer differing levels of complexity so that deployers may make query pages simpler and easier to use or more flexible and feature rich depending on the situation If you wish to use MartAnalysis please keep the number of attributes and or filters in the config as few as possible as large number of attributes and or filters will result in queries that may not scale MartSearch is not yet fully supported and will become available in the near future 5 12 1 MartSearch MART SEARCH llba D Go biossgsmart 36 5 12 2 MartAnalysis VIEW msd config aig VIEW XML 2 HELP 1 SELECT DATASETS 2 RESTRICT SEARCH 0000 0000 MSD protein structures Experiment type Species name s comma separated Resolution greater than Resolution less than Assembly Class Assembly Type Go Diosseemart Electron diffraction Electron microscopy Electron tomography Fibre diffraction electron Infrared spectroscopy Single crystal X ray diffraction Solid state NMR Theoretical model ses Choose rs K Choose P 37 5 12 3 MartForm Sg Dui Fibre diffraction electron Fibre diffraction X ray GO bios smart 38 5 12
62. s POIN E 43 Deploy BIOMart W CO SCE VCP E 44 Arrgt GS Deploy NG E 45 SCC E 46 8 1 Secure web connections HT TPS E 46 E geet 46 oe ENT em 50 9 1 Creating a new E o dT eee ns ene nT ne eee nee Teor 50 9 1 1 Front end files client side component eene nnne 50 9 2 oii c E Y 51 92 Usmge thenew pbi E 51 J3 Am duvaesdexanmlgicsssauaiusu maim quie lu t ihn Mu INA E ere 53 9 54 Chase DIEI DBE senec irt Evo en m 53 10 11 9 3 2 Modify index jsp RERO 53 ee Newa yeon EO eaa E e M M O EE 54 Tode Nowa en Og E eee ere 54 Tee le 56 9 4 Custom Processors server side component ressent nnns 56 Preconfigured Portal Deployment e eereeerereenn nennen nnns 59 JU WMEBIOC o p 59 10 1 1 Changing Connection en 59 10 1 2 Quick deele Vd TEE 59 10 1 3 Configuring the header footer and sidebar sss 60 10 1 4 Configuring the location dropdown esent ntnnes 60 EUM TE uisi Y 60 IEN E Advanceddeploy Til E 61 EE Y ua m 63 11 1 Query IMI E 63 MMs EE 63 RK RE AO 65 11 3 1 Specifying Response BOTIHOLU reet iere tte cite catt ttn Pugna duci edere 65 d IRSE e E e E eee ee ee ee ee ee ee eee 66 Een REENEN
63. scribed in 11 5 1 Data queries are carried out using SPARQL SPARQL queries can be constructed using the web interface and then submitted via the REST interface to retrieve the results in SPARQL XML format as described in 11 5 2 11 5 1 Meta Data Retrieval Working with Ontologies Ontologies are generated within MartConfigurator For new access points an ontology is automatically generated and no manual interactions have to be carried out in MartConfigurator For existing access points an ontology can be generated retrospectively Generating an ontology for an existing access point bios smart 79 o Portal User group anonymous T SCH defat da Add Access Point Name Description Source 9 my access point mv access point Homo sapiens genes GRCh37 Edit Rename Remove Cut Copy Paste Properties v Activate Hide Readonly Set Group All attributes and filters are now part of the ontology as OWL DatatypeProperties They are part of the OWL class that is named after the access point itself my access point in this example The OWL ontology can be accessed in a deployed mart under the URL http host martsemantics accesspointname ontology For the access point given above the URL is http localhost 9000 martsemantics my_access_point ontology The ontology can then be inspected using prevalent OWL tools such as Protege http protege stanford edu Class View in Protege bios
64. should be the same as the database server for your non materialized data source When these fields have been entered click Generate SQL This will bring up the MartRunner jobs window biossgsmart 20 A A Jobs available 1261493979561 3 Job ID number 1261493979562 15 1261493979563 37 JDBC URL Username 1261493979564 37 1262620564991 37 1262634934134 37 Contact email address 1262634934135 37 1291738800705 245 Start job Preserve temporary tables 1291738800706 178 e 1291738800706 178 178 Parallel threads 1 Update Status Time taken Started Finished Messages Refresh gt In the left hand panel labeled Jobs available there will be a list of numbers Green numbers are successfully completed jobs red numbers are jobs that aborted due to errors pink numbers are jobs that have not been started and blue numbers are jobs that are in progress Your job should be the last on the list and in pink if this is your first time materializing a schema it will be the only job Select it by clicking on the entry in the left hand panel then click Start job Depending on the size of your database this may take several hours You can update the status of the job by clicking on the Refresh button in the lower left corner of the window When the job number turns green it is complete and you may close the window Once the job is complete you can set the database to quer
65. sion 0 8 untitled xml Weak ai m D sacs P Add Source default D report W L 3 MSD Protein Structures dp Add Access Point V Show hidden configs V List View Name Group 9 msd config MSD Protein Structures To test the registry you can now click on the Start Server button in the upper right eoo MartConfigurator Version 0 8 untitled xml AAA 0101 sp Add Source default Bl report W 4 MSD Protein Structures P Add Access Point V Show hidden configs List View Name msd config MSD Protein Structures You will be prompted to save the registry file you ve created and after doing so the server will be deployed on your local machine port 9000 Your web browser should open to the home page automatically when the local server is ready bioes smart eo 9 Your Site Title Here Home Not logged in Login Dataset summary MSD Protein Structures You can also deploy BioMart server from the command line on a server First from the File menu save your registry as quickstart xml t is recommended that you save them to the registry subdirectory of the directory where you installed BioMart Next you must configure the BioMart server In a text editor open the biomart properties file located in the dist subdirectory of the directory where you installed Biomart In the HTTP settings section change the http host property to 0 0 0 0 and c
66. smart 80 Active Ontology Entities Classes Object Properties Data Properties Individuals OWLViz DL Query OntoGraf Class hierarchy inferred Usage Class hierarchy WEI A 1 x Annotations 3 hsapiens gene ensembl Cmy access point Mi Description een Equivalent classes o Superclasses o Inherited anonymous classes Members Oo Keys o Disjoint classes o Disjoint union of o No Reasoner set Select a reasoner from the Reasoner menu M Show Inferences Property View in Protege biossssmart 81 Active Ontology Entities m uniprot_swissprot weuniprot swissprot accession s validated swwallaby chrom end swallaby chrom start s wallaby chromosome mewallaby_ensembl_gene mewallaby_homolog_dn mewallaby_homolog_ds mewallaby_homolog_ensembl_peptide mewallaby_homolog_perc_id mewallaby_homolog_perc_id_rl mewallaby_homolog_subtype eewallaby_inter_paralog_dn wewallaby_inter_paralog_ds mewallaby_inter_paralog_perc_id mewallaby_inter_paralog_perc_id_rl mewallaby_inter_paralog_subtype mewallaby_orthology_type mewikigene_description mewikigene_id mewikigene_name mewith_acarolinensis_homolog mwwith affy hc g110 wwwith affy hg focus wwwith affy hg u133 plus 2 eewith_affy_hg_ul33a mwwith affy hg u133a 2 wwwith affy hg u133b mewith_affy_hg_u95a mwwith affy hg u95av2 wwwith affy hg u95b mwwith affy hg u95c mwwith affy hg u95d mwwith affy hg u95e mwwith affy huex
67. stallation directory Then from the dist subdirectory run the following command A new portal configuration file with a time stamp as part of its name something like icgc5 2011 56 07 17 56 59 xml will now be generated with updated information to point to your local database A key file named as cgc5 201 1 56 07 17 56 59 will be generated too This key file is used to encrypt decrypt the passwords in the xml file so you can share the xml file with others without worrying about exposing password 10 1 2 Quick deployment Once previous step is done you can quickly deploy the BioMart server with your data using default settings by Jscripts biomart server sh start bios smart 59 This will create an instance of the BioMart web tool on your local machine You can access it manually by navigating to http localhost 9000 in a browser window Once your test instance is deployed please test that querying returns results for both your dataset s and for datasets from other ICGC members For advance deployment please refer to 10 1 6 10 1 3 Configuring site appearance The BioMart installation directory contains a directory named themes in which sets of pre configured site web pages header sidebar footer etc are provided An cgc5 theme is included with the current BioMart release To enable a theme for your ICGC portal site before you ve run ant to build BioMart edit the file ant properties in the BioMart insta
68. t header into the request biossssmart 65 e application xml for XML e application json for JSON Appending the request with the corresponding file extension e xml for XML e json for JSON For Example the following both return the response in JSON format Curl H Accept application json http dcc icgc org martservice marts e curl http dcc icgc org martservice marts json Note The default format is XML so the method http dcc icgc org martservice marts will return XML unless the Accept header specifies otherwise 11 3 2 Status Codes The following status codes are returned from the REST API e 200 OK Success e 400 Bad Request The request was invalid The accompanying message will explain why 404 Not Found The requested resource was not found 405 Method Not Allowed The method was invalid for this request e g Using POST for a GET request e 500 Server Error Something is broken Please send a message to the mailing list users biomart org with the request and any accompanying response message 11 3 3 Resources The following is a list of resources available from the BioMart REST API 11 3 3 1 Portal Returns the root GUI Container containing all child Containers and associated Marts URL martservice portal Method bios smart 66 GET Parameters guitype optional Restricts returned containers to only the specified GUI type e g martform Returns Root GUI Container object
69. t the line break is not actually present and is inserted because of the length of the page Be sure not to add any extra spaces or characters after the commas or it will not work Next in the registry of Server A in the Data Source Management dialogue find the connection to Server B or create it if it does not already exist In the key column enter the string you created in the last step Data Source Management Dataset Display Name Connection Parameters Database Schema Hide Key SERVER A https bm test res oicr on ca 9077 biomart martservice false 2d25dc8bb Breast Carcinoma W https bm test res oicr on ca 9077 biomart martservice false i3b Malignant Melanoma https bm test res oicr on ca 9077 I biomart martservice false Liver Cancer NCC JP https bm test res oicr on ca 9077 biomart martservice false bios smart 48 Server A will now connect securely to Server B using the credentials of the selected user You may wish to do the same in the reverse direction if the Server A connects to Server B and you would like it be over secure connection biossgsmart 49 9 External Plugins This section will outline the steps required for writing third party plugins for BioMart It is assumed that you already have experience with MartConfigurator and server deployments This section will assume that your server is deployed locally on http localhost 9000 If this is not the case pleas
70. uence mart 8 f fungal mart 8 f fungal sequence mart 8 f metazoa genomic features mart 8 f metazoa mart 8 metazoa sequence mart 8 C plant mart 8 f plant sequence mart 8 C protist mart 8 C protist sequence mart 8 C htgt REACTOME C WS220 testing Clicking the Aad button at the bottom of the window will import each checked dataset as a separate data source biossgsmart 15 5 4 Adding a new RDBMS Source The RDBMS type sources are divided into two sub types Relational Mart and Source Schema 5 4 1 Adding a new Relational Mart A Relational Mart can be used to import an already existing materialized mart To add a new Relational Mart first add a new data source by clicking on the Add Source button Select RDBMS from the Type dropdown select Relation Mart radio button and then select your database type from the Database type dropdown Enter your database connection parameters including username and password and then click the Get button A list of available marts will show in the left panel AO Add Data Source Type RDBMS HH Name D group Database type MySQL Hd M Using MyISAM Source Schema 9 Relational Mart Host martdb ensembl org E Port 5316 Database JDBC URL jdbc mysql martdb ensembl org 5316 Username anonymous Password Get Schemas Tables vegd Tat 4o _ vega mart 49 f vega mart 50 vega mart 51 vega mart
71. vice getPortalServiceImplPort Mart mart port getMarts null get 0 System out println String format Using mart Ss n mart getDisplayName Dataset ds port getDatasets mart getName get 0 System out println String format Using dataset Ss n ds getDisplayName Attribute attr port getAttributes ds getName null null get 0 System out println String format Using attribute Ss n attr getDisplayName String query String format DOCTYPE Query gt Query client javaclient processor TSV Limit 10 header 1 gt Dataset name s config s gt lt Attribute name s lt Dataset gt lt Query gt ds getName mart getConfig 4 4 aLLtr gertName System out println Query is query String results port getResults query System out println Results are n results Finally compile and execute the BioMartSoapClient class javac BioMartSoapClient java java BioMartSoapClient bios smart 77 You should see some data output from the Java class 11 4 2 Accessing SOAP API Using Python In Python you can use the suds package easy install suds which will read the WSDL and allow you to interact with the SOAP API sample Python Client biomartclient py biomartclient py Y vv v from suds client import Client client Client http localhost 9000 martsoap wsdl mart client service getMarts None
72. y the materialized mart by right clicking the data source and unchecking the Query Source Schema option ANDO File O Source WY default dh Add Source F3 transcript Dataset Source Management Update Link Info Link Index Remove Rename Schema Editor Materialize v Query Source Schema biossgsmart 23 5 7 Adding marts from Registry File The Registry File option in Add Source panel facilitates the import of a BioMart vO 7 registry file that in turn points to various MartDBLocation and MartURLLocation based sources The xml file can be specified using the choose file button and subsequently selecting all or a selection of marts to be imported into MartConfigurator using Add button The software will automatically run the backwards compatibility to transform BioMart vO 7 sources to v0 8 AOO Add Data Source Type Registry File HH Name A choose file Marts Datasets Z msd url M msd f htgt url REACTOME url biossgsmart 24 5 8 Creating and modifying an access point To create an access point click on the Add Access Point button in the Portal section default BB report B M Show hidden configs V List View Name Description Source 9 msd config msd MSD Protein Structures 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

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