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BioMart 0.9.0 User Manual

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1. 50 UI VCCI mew DING ec tee cate ces cate cetaceans gee ol cee ee Pam trei 50 9 1 1 Front end files client side component essit tentent ttn 50 ITa Sp PT 51 92 SING DE HOM DIUDI cm teret mieu uium POMPEII MEI CMM eee cee 51 93 Anadvanced EE eege 53 Lu Change DEIUOIDIAU BE eie tt He n UTE N UMEN UE rier cere 53 OP MEE AIUTO erie 53 biossgsmart 2 10 11 12 poU EE Ee 54 Daa NewJavasSc ripi le ate emt AEAEE A TIMIME CR er UEM 54 Da KE e 56 9 4 Custom Processors server side componentl ENEE 56 EXTENDING QUERY HANDLING geegent 59 Ed WE mne dqese muerte E Pu cu Im A crt EO step zen scire sicise eke 59 EE 59 103 Implementing G DINO rE 63 AOD Dependency InjeetlOFLuueanaenene atm stuttgart pu emaceeteeetenetttaes 64 JI MEE cE M R 65 10 4 1 BED format downstream upstream support ENEE 66 PRECONFIGURED PORTAL DEPLOYMENT e nernn nennen nennen nnn nnn nenne nnns 67 Ee 67 11 1 1 Changing Tee 67 TILZ le 67 1113 e Ee 66 11 1 4 Configuring the location dropdown sistat tnnt tnnt tana 68 Re COMI eae 68 ILLO TOV GIGLI e 69 BPIOMART APE a E E E 71 ECG E a d 71 LE ee 71 YAS S TTA E 73 12 31 Specying Response FOFBIOUsm esatta ae toti een dard dS 73 RE CLES e 74 E EE 74 AL E Ee E 74 EE 76 JU Ao So E 77 P E e 78 12 09 9 E 79 JM r o
2. Select the attribute s on which to base the link in both sides by double clicking Multiple attributes can be selected to form 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 eoo File P Add Source MSD protein structuv777 Dataset Source Management fJ Danio rerio genes i Update 3 Mus musculus gend IST RN Link Index Remove Rename L3 Homo sapiens gene Schema Editor Materialize Query Source Schema bios smart 39 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 OQO Link Management Dialog Data source MSD protein structures HH v L3MSD protein structures v L3 Mus musculus genes NCBIM37 msd mmusculus_gene_vega link v 3 Homo sapiens genes GRCh37 p2 Z msd hsapiens_gene_vega link 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 h
3. M 80 2 945 EE 82 ET EST D c erty 63 T2 e e 63 9 420057010 eee ne ee ene ree ae 84 DT MEE NET NBUSITNULIT 64 1242 Accessing SOAP API Using Pyth nausea dte do vitet ae een ne eeaenonivess 86 EE Ee 67 12 5 1 Meta Data Retrieval Working with Ontologies es 67 12 5 2 Semantic Querying Using SPAR AT 91 PO JO 0 93 D DI ee E 93 UON PEE e OR 93 D OA OO CTC Oi eebe 94 120 E Sm 0 sse cum MMMMEDUIU 94 EE E suse enim imNDUE MM LM E 94 E E SRHOTS ueetauaven oue Riu EuGH UM 95 gor NP OMM cvi inim 95 bios smart 3 13 25 NNMERO Iac 96 I0 EE TER 96 L E TU C eee 97 12 6 2 1 Set Processor trn tita teta aa ea aa a aa aba aao sooo Ao ooo 97 LeDcc SOLLI E 97 12073 IEB DIe JHOSU OI sonantem A EEURLI I OIM IEEE 97 12 6 2 4 Set Client NAM ssreiscsecssesssceressesscesessceserseieresssiscestesseasesnesorsesssnsesneserosesserbsovissssdsacaveasestesosssaveast 98 12 0 2 9 AU DUO OSEE secciones mE n EE Mem ME EE EU 98 12D QU IVLDUAMIOS EE 98 ESO A O ME 98 126 32 Tele RE Keier 99 12633 e e E 99 LOA iro 1 cue 99 15 09 Ee GE ee EE ele 100 PIT PLAUT UI 101 TROUBLESHOOTING INSTALLATION rrr nnn nnn 102 E EE e 7 c 102 VENE NEED 0 575 rEE
4. 102 TS ER ee TE 102 SW MEE En e m ase 103 bios smart 4 1 Prerequisites Software Java 1 6 Ant and Git 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 git branch 0 9 0 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 eo00 File de Add Source In the Add Source Wizard window that appears click the Next button Choose data source type URL Enter or choose a source profile Cancel Next Add Source Wizard biossgsmart 6 and Next button again to to connect to BioMart central portal Add Source Wizard protocol http O version 0 8 host www biomart org port 80 path biomart martservice user password Key oauth Cancel lt Back Next Finish
5. v 9 msd config v Di root v D ATTRIBUTES v iH Features v amp MSD ENTRY DATA meet 2 Title 9 Experime Copy Header Cut Authors Remove 9 Keywords Create filter 2 Submissic Release c Move up Move down Show all references 2 R Work gt E MSD ASSEMBLY DATA displayname PDB ID s description SSS met LI bios smart 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 M 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
6. ja Choose un iue Choose ain 37 5 12 3 MartForm e DATASETS s Des iz 8 emm MSD protein structures Fibre diffraction electron Fibre diffraction X ray Go bios smart 38 5 12 4 MartWizard Datasets Filters Output Restart Prev FEATURES MSD ENTRY DATA M PDB ID s O Experiment Type O Authors O Submission Date Resolution O R Work MSD ASSEMBLY DATA O Assembly Type 5 12 5 A root 4 ATTRIBUTES MSD ASSEMBLY DATA MSD CHAIN DATA EXTERNAL IDENTIFIERS HETGROUP O Title O Header O Keywords O Release Date LJ Space Group O Assembly Code MartExplorer Datasets Filters Output nma Restart Prev M PDB ID s O Experiment Type Authors O Submission Date CJ Resolution EJ R Work MSD ENTRY DATA C Title O Header O Keywords O Release Date CJ Space Group bios eeiart 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 Oe Attributes PDB ID s OO 39 5 13 User management BioMart supports multi user access such that configs can be individually set to be visible or hidden for different gr
7. function Multiple Chromosomal Regions Chr Start End Strand H3 Background EH Cut Off Value chromosome name start end strand bios smart o a 62 Note that the function assigned to a filter list or an attribute list will be inherited by all the filters and attributes respectively of that list 10 3 Implementing a Dino A dino is a Java class that implements the Dino interface defined under the org biomart dino dino namespace There are few methods that must be implemented and they can be found in the Dino interface file As said before a dino expresses its requirements that is the input for each query in a declarative way This is done through the Func Java annotation defined under the org biomart dino annotations namespace that has two attributes id optional Example public class Converter implements Dino Func id genes String source gFunc id Convert to convertTo Func id annotation optional annotation In this example we created a Converter dino stating that the query must contain two elements with function property value equal to genes and convert to and a third one optional with property value annotation At the moment that a new query with same configuration as the one the Converter dino has been attached to comes in a new instance of the class is created provided with the Query object and run The binding of the query element values to the state
8. 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 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 7 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 instal
9. Add Source Wizard A list of available marts will appear in the left panel Click on msd to select and check it Type URL Name group Host http www biomart org Port 80 Path biomart martservice user password Marts Datasets C bacterial mart 8 M msd f bacterial sequence mart 8 f fungal mart 8 fungal sequence mart 8 metazoa genomic features mart 8 f metazoa mart 8 Ld f metazoa_sequence_mart_8 C plant mart 8 f plant sequence mart 8 C protist mart 8 f protist sequence mart 8 C htgt f REACTOME C WS220 testing bios smart 7 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 V defaut dh Add Source f3 MSD Protein Structures In the right hand panel click the Add Access Point button bios smart 8 eno MartConfigurator Version 0 8 untitled xml Y defaut O lOisutsees P Add Source E defaut P report W L 32 MSD Protein Structures V Show hidden configs 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
10. Name Description Source Group msd_config msd MSD Protein Structures The File menu either at the top of the window or 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 Add 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 bios smart 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
11. Using attribute Ss n attr displayName query DOCTYPE Query Query client pythonclient processor N TSVN limit 10 header 1 gt lt Dataset name s config s gt Attribute name Ss lt Dataset gt Query ds name mart name attr name print Ouery is query results client service getResults query print Results are n results Execute the Python script to see the output python biomartclient py biossgsmart 86 12 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 described in 12 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 12 5 2 12 5 1 Meta
12. 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 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 95s 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 dist 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 GQ OO HHA Bloalines 28264 un Bookmarks Employee guide B
13. connecting lines The columns in a given table can be shown by clicking the Show co umns button for that table A table column or relation can be hidden by right clicking on the object 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 script
14. Authors Experiment Type Header Keywords Resolution Space Group L Cancel 9 t Select The attribute you select will be used as the key for the report page and a hyperlink will be created on this attribute for linking to the report page Clicking biossgsmart 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 M Bookmark XML SPARQL QJava Download data 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 1031 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 3 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 SNCP GP CP AP TP GP G 3 Click on the PDB
15. C group Host http www biomart org Port 80 Path biomart martservice user password key C bacterial mart 8 f bacterial sequence mart 8 f fungal mart 8 f fungal sequence mart 8 metazoa genomic features mart 8 f metazoa mart 8 f metazoa sequence mart 8 f plant mart 8 f plant sequence mart 8 C protist mart 8 C protist sequence mart 8 C htgt f REACTOME C WS220 testing 8 Datasets Clicking the Aad button at the bottom of the window will import each checked dataset as a separate data source bios eeiart 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 L3 6 Add Data Source Type RDBMS Hd Name D group Database type MySQL Hd vi Using MyISAM Source Schema 9 Relational Mart Host martdb ensembl org Port 5316 Database JDBC URL jdbc mysql martdb ense
16. Returns List lt org biomart api lite Dataset gt biossgsmart 96 12 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 12 6 2 1 Set Processor Method setProcessor Parameters 9 Nonnull String processor Sets the processor that the query engine will run through Default is TSV Returns org biomart api Query 12 6 2 2 Set Limit Method setLimit Parameters int limit The number of result rows to be printed Returns org biomart api Query 12 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 DIO emer 97 12 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 12 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 config The config of the Mart Please specify this if it is non empty Returns org biomart api Query Dataset 12 6 3 Query Dataset The org biomart api Query Dataset o
17. be created and shown in the right hand panel ADP MartConfigurator Version 0 8 untitled xml Y defaut Wl User group C anonymous EI i ep Add Source default Bl report BB 4 MSD Protein Structures ep Add Access Point V Show hidden configs List View Name ipti Gr Q msd config MSD Protein Structures Start Server oup To test the registry you can now click on the Start Server button in the upper right biossgsmart 9 ECHO MartConfigurator Version 0 8 untitled xml 3 MSD Protein Structures S Group 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 Your Site Title Here Home Not logged in Login Dataset summary MSD Protein Structures TT Powered by DIOS smart ee 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
18. begins with a period You may biossgsmart 69 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 Dioseeermart 70 12 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 12 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 processor any valid processor name e g TSV e limit the number of rows to return 1 for no limit e 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 config optional the config 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
19. cgc5 201 1 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 11 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 Dio mart 67 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 11 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 installation directory and change the property theme from default to your theme of choice theme icgc5 After performing the BioMart build the dist web includes
20. element must contain at least one lt Attribute gt element e name name of attribute Sample Query XML Query client processor TSV limit 1000 header 1 gt lt Dataset name hsapiens gene ensembl hopkinsBreast3 config hsapiens gene ensembl Filter name biotype value miRNA Attribute name ensembl gene id Attribute name cancertype Attribute name description gt Attribute name start position Attribute name end position lt Dataset gt lt Query gt 12 2 Processors 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 processors are available in BioMart biossgsmart 71 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 valuelc wvaluezc 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 T
21. filter with function property equal to sets This filter must be of the same type of the bed regions filter bios smart 66 11 Preconfigured Portal Deployment 11 1 ICGC 11 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 lists oicr on ca for your DATASETNAME etc config oauth openidz https me yahoo com a lyINRct235wrollONtQMUcKwenvgzlUqbyaA datasets dataset name DATASETNAME database YOURDBNAME dbhost YOURSERVER dbport YOURPORT dbuser YOURUSER password YOURPASSWORD gt lt datasets gt lt config gt Save this file as update xml in the dist subdirectory of your BioMart installation directory Then from the dist subdirectory run the following command Jscripts updatelCGC sh registry icgc5 xml update xml A new portal configuration file with a time stamp as part of its name something like
22. hsapiens gene ensembl config addrilter chromosome name I addAttribute ensembl gene id end query getResults System out System exit 0 Compile the code and run it javac cp QueryExample java java cp QueryExample bios smart 101 13 Troubleshooting Installation 13 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 13 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 if SJAVA HOME then JAVA HOME bin Java version else java version fi java version l 60 0 242 Java rM SE Runtime Environment build 1 6 0 22 b04 307 10M5201 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 June 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 13 1 2
23. mE L H x Annotations o Q hsapiens gene ensembl C my access point Description iif OE Equivalent classes Oo Superclasses Inherited anonymous classes Members o Keys o Disjoint classes o Disjoint union of Oo No Reasoner set Select a reasoner from the Reasoner menu M Show Inferences Property View in Protege bios smart 89 n g ontology http 10 0 3 31 9000 martsemantics mm access point ontology rn 88 Qa Active Ontology Entities Classes Object Properties Data Properties Individuals OWLViz DL Query OntoGraf Data property hierarchy Dee Ta amp x seuniprot swissprot sweuniprot swissprot accession mevalidated mewallaby_chrom_end mewallaby_chrom_start mewallaby_chromosome mewallaby_ensembl_gene mewallaby_homolog_dn mewallaby_homolog_ds mewallaby_homolog_ensembl_peptide mewallaby_homolog_perc_id mewallaby_homolog_perc_id_r1 mewallaby_homolog_subtype mewallaby_inter_paralog_dn mewallaby_inter_paralog_ds mewallaby_inter_paralog_perc_id wwwallaby inter paralog perc id rl swallaby inter paralog subtype mewallaby_orthology_type mewikigene_description mewikigene_id mewikigene_name esewith_acarolinensis_homolog eewith_affy_he_g110 eewith_affy_hg focus eewith_affy_hg_u133_plus_2 wwwith affy hg u133a mwwith affy hg u133a 2 mwwith affy hg u133b wwwith affy hg u95a wwwith affy hg u95av2 mewith_affy_hg_ u95b mwwith affy hg u95c
24. main xml Portal portal new Portal factory Lisr Mart marts portal getMartsimull ovstem out printlin 5String tormat GOL marts marts size List Dataset datasets portal getDatasets marts get 0 getName System out printin String format Got s datasets datasets size List lt Filter gt filters portal getFilters datasets get 0 getName marts get 0 getConfigName null System out println String format Got s filters filters size List Attribute attributes portal getAttributes datasets get 0 getName marts get 0 getConfigName null 5vstem out printlin String ftormat Got s attributes attributes size System exit 0 Compile the code and run it javac cp PortalExample java java cp PortalExample bios smart 100 12 6 4 2 Querying The following is a runnable Java class that demonstrates how query execution can be done QueryExample java import org biomart api Portal import org biomart api Query import org biomart api factory MartRegistryFactory import org biomart api factory XmlMartRegistryFactory public class QueryExample public static void main String args MartRegistryFactory factory new XmlMartRegistryFactory path to xml Portal portal new Portal factory Query query new Query portal SetProcessor TSV SetClient test SetHeader true SetLimit 10 addDataset hsapiens gene ensembl
25. mwwith affy hg u95d mwwith affy hg u95e mewith affy huex 1 0 st v2 wwwith affy hugene 1 0 st v1 wwwith affy hugenefl Usage Annotations Dee Annotations Functional Domains intersection Ranges Equivalent properties Super properties Disjoint properties Characteristics OA Description ESSI S No Reasoner set Select a reasoner from the Reasoner menu Class Dependencies in Protege Showing Dataset Usage Di eeeel Tall M Show Inferences 90 CH ontology http 10 0 3 31 9000 martsemantics my access point ontology http localhost 9000 martsemantics my access point ontology eis ontology http 88 Q Active Ontology X Entities Classes Object Properties Data Properties Individuals OWLViz DL Query Class hierarchy Dataset DSS i OntoGraf f v G Thing hsapiens gene ensembl C my access point ID ESL Ed t j Ea JD ASIA WISIS SKI Ee e my access point l hsapiens gene e nsembl Thing ac Ii Y EN hsapiens gene e No Reasoner set Select a reasoner from the Reasoner menu v Show Inferences 12 5 2 Semantic Querying Using SPARQL SPARQL queries can be generated 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 lt gt REST SOAP 2 SPARQ
26. myplugin directory 9 3 1 Change plugin URL We will now append additional information GUI container 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 bios smart 53 lt doctype html 80 page language java 8 page contentType text html charset UTF 8 gt html lang en gt head title My Plugin lt title gt link type text css href styles css rel stylesheet lt head gt body h1 My Pluginc h1 div id gui gt lt h2 gt Selected GUI Container lt h2 gt lt div gt div id mart gt lt h2 gt Selected Mart lt h2 gt lt div gt lt script type text javascript erc 78 lib jquery l 4 2 72min 1S lt 7 eer lt script type text javascript src script js gt lt script gt Ssocripto 5 initialize script body html 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 font size 12px background color eee Margin Je hl font size 24px h2 T dolor 7555 gui
27. of the dino in this case source convertTo and annotation doesn t happen automatically but the dino instance itself does it using the Binding utility class In this way a dino has greater control over the binding and can bind element values to its state variables multiple times per request Follows an example biossgsmart 63 0verride public Dino setQuery Query query 4 query return Override public void run OutputStream out throws Exception List lt Field gt myFields Binding getAnnotatedFields getClass List lt QueryElement gt elements q getQueryElements List lt QueryElement gt boundEls Binding setFieldValues myFields elements creates the binding table Key String function id Value QueryElement Element the element metaData setBindings myFields boundEl1s doRun 10 3 1 Dependency Injection is used for dependency injection and the module that defines injectables for dinos is under the org biomart dino namespace and is called DinoModule surprise biossgsmart 64 10 4 Enrichment Note that functionality could change in the future The Enrichment Dino is an extension that given a set cutoff an optional background and other requirements conducts an enrichment process using a C program written by Prof Paolo Provero of University of Turin and returns the results with format as specified by the processor query parameter if the head
28. organized into GUltabs which determine how they are presented to the user The current GUltabs are listed in E and a new GUltab 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 bios smart 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 7 0 Add Data Source Type URL ai Name el group Host http www biomart org Port 80 Path biomart martservice Marts Datasets Cabot MD 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
29. subdirectory of your BioMart installation directory will contain a file header htm l 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 11 1 4 Configuring the location dropdown To enable the locations dropdown on the homepage and add your site you must open the file ocations 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 11 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 bioss smart 68 lt 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 will 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 su
30. the existing data sources to choose which one you would like to make an access point for After giving the new access point a name of your choice it will appear in the GUI tab Double clicking on the access point icon will open a new window that allows you to modify the access point bios smart 25 L Import from sources Search lal oS gt root datasethidevalue master readonly assword m 3 z Lo nw E a Qc m nm 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 bios smart 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 ll v 9 msd config v tB root v i8 ATTRIBUTES v Gi Features amp IEE2UEAES WES E MSD ASSEMBLY DATA 8 MSD CHAIN DATA H3 EXTERNAL IDENTIFIERS 8 HETGROUP 8 JOURNAL gt gt FILTERS maxcontainers maxattributes bios smart 27 Any object can be hidden from the end user by right clicking on that object and selecting Hide from the menu is Mem gt Import from sources Search ad
31. the password is P sswoOrd The administration page has an Add New Consumer button which will allow you to create an access token for Server A BioMart Administration OAUTH CONSUMERS Add New Consumer Y T Powered by biosss smart ee Add OAuth Consumer Name required Description Key required 401f91ac325157aaf03c1408e387a7bf Secret required 0a2b4eBc8B618224b3aa4dcBab293cBac245e3e57 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 A7 BioMart Administration OAUTH CONSUMERS x SERVER A Description Key 2d25dc8bb022ce496d23f8d8ac95a815 Secret 7ce4ab04ad4ad3ad1dde6c3b6a24f9a558fa4d0a Add New Consumer eg 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 ab83d6b086163a04a50ee1f3a3d767de Access token secret 9e2e908754dce0a0d40dc277f374d1f7 Close You must combine these four strings separated by commas So in this case it
32. transcript supporting feature C translation attrib C translation stable id Cl unconventional transcript association f unmapped_object C unmapped_reason C xref Lal In the right panel select the table s that will become you main table s and click Add to create your data source 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 DAA source target Hide masked dependent xref omo sapiens vega 61 exon transcript homo sapiens vega 61 37f d X ditag feature X homo sapiens vega 61 37 misc feature density feature homo sapiens vega 61 37 b dna align feature homo sapiens vega 61 37 dnac homo sapiens vega 61 37 x homo sapiens vega 61 37 e v tT jexon d external synonym E B m homo sapiens vega 61 371 0 7 homo sapiens vega 61 37 mapping session misc set y X homo sapiens vega 61 37 homo sapien Show columns Show columns Show c Show columns m Ra Show columns HJV NNS 7 M A d The Schema Editor shows database tables pink boxes as well as the relations between these tables
33. will see later on 12 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 93 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 12 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 12 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 12 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 biossgsmart 94 List lt org biomart api lite Dataset gt 12 6 1 5 Filters Returns a list of Filters Method getFilters 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 conta
34. would be 2d25dc8bb022ce496d23f8d8ac95a815 7ce4abO4ad4ad3ad1dde6c3b6a24f9ab558fa4dOa ab 83d6b086163a04a506ee1f3a3d767de 9e2e908754dce0a0d40dc2771374d1f7 Note that 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 Key SERVER A https bm test res oicr on ca 9077 biomart martservice 2d25dc8bb Breast Carcinoma W https bm testres oicr on ca 9077 biomart martservce false 3b Malignant Melanoma https bm testres oicr on ca 9077 biomart martservice false Liver Cancer NCC JP https bm testres oicr on ca 9077 biomart martservce fale 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 bios smart 49 9 External Plugins This section will outline the steps required for writing third party plugins for BioMart It is assumed
35. 7a homo sapiens vega 57 37b homo sapiens vega 58 37c homo sapiens vega 59 37d homo sapiens vega 60 37e f homo sapiens vega 61 37f CH 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 Type RDBMS E Name DH group Database type MySQL Musing MyISAM 9 Source Schema Relational Mart Host ensembldb ensembl org Port 5306 Database JDBC URL jdbc mysgl ensembldb ensembl org 5306 Username anonymous Password f partitioned Schemas homo sapiens vega 49 36k f homo sapiens vega 50 36l f homo sapiens vega 51 36m f homo sapiens vega 52 36n homo sapiens vega 53 360 homo sapiens vega 54 36p f homo sapiens vega 55 37 homo sapiens vega 56 37a f homo sapiens vega 57 37b f homo sapiens vega 58 37c C homo sapiens vega 59 37d f homo sapiens vega 60 37e homo_sapiens_vega_61_37f C stable id event f supporting feature ivi transcript C transcript attrib C transcript stable id C
36. A transcript ID VEGA protein ID Canonical transcript stable ID Description 2 Chromosome Name Gene Start bp Gene End bp Strand 2 Band Transcript Start bp Transcript End bp M en nm Ap gene vega displayname hsapiens gene vega datasetdisplayname POD 1 1 1 metainfo uu emm v root v 3 ATTRIBUTES v amp Features v amp 3 MSD ENTRY DATA PDB ID s Title 2 Experiment Type 2 Header Authors 2 Keywords Submission Date Release Date Resolution 2 Space Group R Work gt 3 MSD ASSEMBLY DATA gt 3 MSD CHAIN DATA Property name 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 Source Homo sapiens genes GRCh37 p2 HH v Q hsapiens gene vega v root v amp ATTRIBUTES v ti Features Y 8 GENE Drag and dro v amp Vega e 2 VEGA transcript ID VEGA protein ID Canonical transcript stable ID Description Chromosome Name Gene Start bp 2 Gene End bp Strand Band Transcript Start bp Transcript End bp r ie _ v 9 msd config v Di root v 3 ATTRIBUTES v amp Features MEIS ENTRY DATA PD
37. B ID s Title Experiment Type Header Authors Keywords Submission Date Release Date Resolution Space Group R Work gt D MSD ASSEMBLY DATA gt amp 3 MSD CHAIN DATA ay e Hide sources 3 Search E EGA gene ID ega Stable ID of the Gene Property Value ent Es MSD ENTRY DATA If no link exists between the sources a Dataset Link Dialog will appear allowing you to create a link sseTart 32 ANO Dataset Link Dialog 2 RefSeq DNA ID 9 RefSeq predicted DNA ID 2 RefSeq RNA ID RefSeq predicted RNA ID 2 RefSeg Genomic ID hsapiens gene vega msd config v tH Features L v 9 msd config v D GENE v Hi root gt 8 Vega v Di ATTRIBUTES v DD EXTERNAL v DD FEATURES v tB External References gt i MSD ENTRY DATA Com MSD ASSEMBLY DATA CCDS ID v Ej MSD CHAIN DATA Ensembl Human Gene 2 UniProt ID s 2 ENST CDS ID 2 Chain code 2 ENST Identical ID 2 Chain length 2 HGNC ID 2 EBI Chain Code 2 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 9 Scop concat 2 Cath concat Q 2 Sws concat 2 EntrezGene ID gt JOURNAL MIM Gene ID gt OD FILTERS gt PROTEIN b I Cteucturaoc la Selected attributes in hsapiens_gene_vega Selected attributes in msd_config UniProt SwissProt Accession UniProt Accession ID s
38. BioMart 0 9 0 User Manual May 2014 biossgsmart Ur am c9 Eet Contents PREREOUI Uoc O 5 DOWNLOAD BIOMANRT E 5 COMPILE AND BUILD BIOMART eneeeeeeeeeeneeeneenn nennen nina annm nisu na aawa aiana anaia 5 JUICE START c esivc ce ctgescnu sex E E E 6 USING MARTCONFIGURAT OR cesssssesssscessessssesssesseorsnseessosseneensesssnrssnessesseneesorsaesenesseesanes 12 31 NEE 12 3 IMPONI SONT CES ee 14 29 Adding anew URG MOT E 14 24 PAGING new RDBMS SOUP CC ise amicus tante et aetatum tu un ux uso A REDI RS 16 541 Addinganew Relational Mab acditudesatietticetibn tr d exiis eet Pe tlc rend ds 16 5 4 2 Adding a new Source Schema Virtual Mart erret 17 5 5 Manipulating a Mart using the Schema Editor senes 20 20 Malerializing a Virual Mat m 21 20 Adding Maris Prom Regis EY FIle sesscsciutut ad EE EER 24 5 8 Creating and modifying an access E 25 on ee E 29 310 Ee ET 31 SAI Cran UID E 35 3127 ChangingtheGUtype or atoni EE 36 aa Ma T NET E EOE AAEE E EEE E 36 SN EE 37 EE 38 VNPT EE Og O EE 39 ro O55 MOFU 0 eege 39 so Ee 40 S4 Hang I CCOSS TE 43 DEPLOY BIOMART WER EEN Eeer 44 CONFIGURE DEPLOY MEN TP iiisexiserkesen End kx iana S ec EE EEN 45 SECURITY Sr 46 Gd Secure Web connections HTTPS usouciesdaseciticntivsten vetas ptite eiiean 46 G2 JdJuthentedted FeHOLO UCCESS on icri od ace a WR M RINT HU RES 46 EXTERNAL BE LL o
39. DL 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 12 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 84 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 biomart api soap Mart import org biomart api soap Dataset import org biomart api soap Attribute public class BioMartSoapClient public static void main String args BioMartSoapService service new BioMartSoapService PortalServicelImpl port service getPortalServicelImplPort 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 Stri
40. 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 bioss smart 87 Portal Usergroup anonymous T An 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 Generate Semantics 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 biossgsmart 88 gt 9 ontology http 10 0 3 31 9000 martsemantics my access point ontology M4 e Active Ontology Entities Classes Object Properties Data Properties Individuals OWLViz DL Query OntoGraf Class hierarchy
41. ID hyper link will bring up the report page as below Home gt report Not logged in Login REPORT PDB ID s llba o Go S ATTRIBUTES PDB ID s 11ba 1 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 GO 0003676 GO 0003824 GO 0004518 HYDROLASE GO 0004519 GO 0004522 GO 0016787 IPR001427 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 E Import from 2 Search lg o oS gt Hi 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 Hide sources Search I7 Source Homo sapiens genes GRCh37 p2 ES LAC ihsapiens_gene_vega v root v amp ATTRIBUTES v Features v Di GENE v Di Vega VEGA gene ID 2 VEG
42. L n Java Download data Working with the generated ontology from above the SPARQL button will for example show bios smart 91 SPARQL Query rdf http www w3 0rg 1999 02 22 rdf syntax ns rdfs http www w3 0rg 20909 01 rdf schema owl lt http www w3 org 2002 07 owl gt accesspoint lt http Localhost 9000 martsemantics my_access_point ontology gt class lt biomart localhost 9000 martsemantics my_access_point ontology class gt dataset lt biomart lLocalhost 9000 martsemantics my_access_point ontology dataset gt attribute lt biomart localhost 9000 martsemantics my_access_point ontology attribute gt Zo al FROM dataset hsapiens gene ensembl WHERE 1 mart attribute chromosome name X mart attribute with entrezgene only mart attribute ensembl gene id a0 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 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 chro
43. 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 102 C 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 214 040 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 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 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 gt 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 ant is not a program To install the latest version of Ant please visit the website http ant apache org 13 2 Testing Environment This BioMart 0 8 release candidate is known to wo
44. 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 Curt http localhost 9000 martservice datasets mart hsapiens gene veg a config Remember one of the Dataset s name e g hsapiens gene vega Retrieve list of Attributes from the Datasets and config bios smart 83 CUI http localhost 9000 martservice attributes datasets hsapiens ge ne vegas amp config hsapiens gene vega config Hemember one of the Attribute s name e g vega gene id Build your Query XML and save it to a file query txt lt DOCTYPE Query Query client 2 biomartclient processor TSV limit 2 header 1 gt lt Dataset name hsapiens gene vega config hsapiens gene vega config Attribute name vega gene id gt Dataset lt Query gt Call the results method to get the data curl data urlencode query query txt http localhost 9000 martservice results You should see the results printed on your terminal 12 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 WS
45. bdirectory 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 11 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 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 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
46. bject contains the Filters and Attributes in a Query Note The Dataset Query object s methods return the object itself This allows for method chaining 12 6 3 1 Add Filter Method DIO smart 98 addFilter Parameters Nonnull String name The name of the Filter 0 Nonnull String value The value of the Filter Returns org biomart api Query Dataset 12 6 3 2 Add Attribute Method addAttribute Parameters Nonnull String name The name of the Attribute Returns org biomart api Query Dataset 12 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 12 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 DIO smart 99 12 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 java util List import org biomart api Portal import org biomart api factory MartRegistryFactory import org biomart api factory XmlMartRegistryFactory import org biomart api lite Attribute import org biomart api lite Dataset import org biomart api lite Filter import org biomart api lite Mart public class PortalExample Public static void main String args MartRegistryFactory factory new XmlMartRegistryFactory Users jhsu
47. contig Smp Gonrclg operation MULTISELECT meta name s Sip SHEET description snp cODnLlg 12 3 3 3 Datasets Lists all the Datasets for the given Mart URL martservice datasets Method GET Parameters config required The name of the Mart to return datasets from Returns List of Dataset objects Sample URL martservice datasets config snp_config Sample XML Response lt datasets gt dataset isHidden false description ptaurus snp displayName Bos taurus Variation dbSNP 130 name btaurus snp datasets Sample JSON Response isHidden false Heme DLaurus snp displayName Bos taurus Variation dbSNP 130 lee Cer eat s DLSUQEUS snp bios smart T1 12 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 snp amp configzsnp config Sample XML Response filters filter isHidden false qualifier type singleSelect description displayName Chromosome name name chr name gt value isSelected false displayNam
48. e 1 name 1 gt SEET SE Sample JSON Response name Che name displayName Chromosome name description e type singleSelect isHidden false biossgsmart 78 aqueliriep s WM filters values f isSelected false name 15 displayName 15 by 12 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 attribute isHidden 2 false linkURL species2 Variation Summary v s value gescription displayName Variation ID name refsnp id lt JAttributes gt bios smart 19 Sample JSON Response hemes Persnp xd displayName Variation ID description s r isHidden false linkURL species2 Variation Summary v s aluet M attributes 12 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 Meth
49. er parameter is equal to false as json otherwise To use this extension the value of the dino property for the configuration must be set to org biomart dino dinos enrichment EnrichmentDino The function property values to set on filters and attributes of a configuration with MartConfigurator for this dino are e Sets the filter that holds the gene list e background optional the filter that holds the gene list acting as background In case of a query without background the whole genome will be used e annotation the attribute that represents the annotation to use There could be multiple attributes with this function per query s bonferroni a Boolean filter that states whether compare the cutoff with corrected p value or not e gene limit optional this should be a filter of type singleSelectBoolean that represents the category of genes to filter the results s homolog optional Note that species translation is supported This extension though needs further information to work within the dist conf dinos enrichment EnrichmentDino json file as you can see from the template file already present it must be specified a table with parameters used for format translation and getting information to build the response for the web GUI e gene a table of parameters to use to format translation and information retrieval that must contain bios smart 65 o gene attribute attribute to use for gene output for
50. er 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 query the materialized mart by right clicking the data source and unchecking the Query Source Schema option ANDO File H Source WY default dh Add Source 3 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 vO 8 AO Add Data Source Type Registry File HH Name C choose file Marts Datasets Cu msd url M msd C htgt url f REACTOME url bios smart 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 defaut M report a LA M Show hidden configs Mi List View Name Description Source 9 msd config msd MSD Protein Structures You will be given a list of
51. es 28264 un Employee guide BuildBot BioMart Stack Overflow BioMart MartView me p ad Qu Recently Bookmarked R by example Grilled Tamarind Sal How Much Is Enough Welcome to Solr Federated search usi RFCAR69 A Pape o Disable v eA Cookies 4 CSS v Forms Images v gu Information L Miscellaneous v sp Outline RI Resize v Y Tools My My Plugin My Plugin Selected GUI Container GUI default Number of marts 2 Selected Mart Mart gene Operation MULTISELECT Me Ysiow X 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 biomar
52. his means that data will be written only when the entire result set is ready which may not be ideal for slower queries Example LOtaL 100 qata 1 Attributel valuela Attribute2 value2a Attribute3 value3a bios smart 12 Attributel s valuelb Attribute2 value2b Attribute3 value3b by Attributel valuelc Attribute2 value2c Attribute3 value3c 12 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 smart description gene vega contig displayName gene vega config name gene vega config GCOonllge gene vega Contig isHidden 2 false meta operation MULTISELECT gt JSON Representation isHidden false displayName gene vega config Gonrlg s Gene vega config operation MUBhTISELECT ne pet TM name gene vega contig description gene vega conlig 12 3 1 Specifying Response Format There are two ways to specify the response format Adding the corresponding HTTP Accept header into the request biossssmart 13 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 E
53. iation ID desoriprion s TM isHidden false T LInkURI S species2 Variation Summary v s value MN attributes l filters Containers bios smart 81 12 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 dataset 1sBridden ralse deseripition heapoiens Snp som displayName Homo sapiens Somatic Variation COSMIC 950 name hsapiens snp som datasets Sample JSON Response isHidden false name hsapilens snp som displayName Homo sapiens Somatic Variation COSMIC description hosprens snp Som bios smart 82 12 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 filenamezresults txt Default is false Returns The result returned from the Query XML 12 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
54. ibility 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 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
55. iner The name of the container you want to return filters for Returns List lt org biomart api lite Filter gt 12 6 1 6 Attributes Returns a list of Attributes Method getAttributes Parameters 0 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 Nullable String container The name of the container you want to return attributes for Returns List lt org biomart api lite Attribute gt DIO smart 95 12 6 1 7 Containers Returns the root Container which containers all subsequent Containers Note Containers and GUI Containers are different objects Method getContainers Parameters 0 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 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 12 6 1 8 Linkables Datasets Returns 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
56. ion p user example e openiD openlD http foo myopenid com biossgsmart 41 This allows remote authentication Currently Gmail addresses are supported as are openlID 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 bios smart 42 5 14 Hiding an access point The current user group is shown and can be changed at the top of the Portal panel Oe default B report BI Sp Add Access Point M Show hidden c Name Description Source msd_confic 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 defaut P 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 vis
57. lation 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 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 bioss smart 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
58. lds 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 bios smart 58 Extending Query Handling 10 1 Introduction In BioMart it s possible to modify how queries are handled through its extension system After an extension is attached to a configuration all the query requests involving that configuration submitted either programmatically through web services or Java API or from the web graphical interfaces will be handled by the extension An extension can express requirements that will be bound to the filters and attributes of the query currently processed in a declarative manner directly inside it s source code How to exactly bound filters and attributes to the requirements is specified by the deployer with MartConfigurator An extension is called Dino 10 2 Configuration To specify a dino for a configuration from MartConfigurator click on a configuration and fill the dino property with the name and namespace of the dino class biossgsmart 59 C Import from sources Search fa v ERT gt Di root Property Value name gene ensembl config 3 1 2 internalname displayname description hide false default EE metainfo C datasetdispla
59. mat translation o description attribute attribute to use to get the description of a gene o other attributes optional list of attributes to use to get other information to build the response for the web GUI annotation a table where each entry has as key the internal name of an attribute used as annotation and as value a table like this o description attribute attribute to use to get the description of an annotation o other attributes list of attributes to use to get other information to build the response for the web GUI 10 4 1 BED format downstream upstream support Note that this functionality could change in the future If you want to support the BED file format upstream downstream for the set you need to set the dino property to org biomart dino dinos EnrichmentDecorator and the function property values to set on filters and attributes of a configuration with MartConfigurator for this dino are bed regions the filter that holds the BED file content e downstram the filter that holds the downstream value upstream the filter that holds the upstream value And finally change the dist conf dinos enrichment EnrichmentDecorator properties file content to s enrichment decorator bed to ensembl output filter the name of the filter with function property equal to regions This filter must be of the same type of the bed regions filter s enrichment decorator upstream downstream output filter the name of the
60. mbl org 5316 Username anonymous Password Get Schemas Tables vegd rrdrt 4o f vega mart 49 vega mart 50 f vega mart 51 vega mart 52 f vega mart 53 vega mart 54 vega mart 55 vega mart 56 vega mart 57 f vega mart 58 vega mart 59 Ii vega mart 60 vega mart 61 Y Abort Addo Once you have made your selection you will be prompted to use the existing config bios smart 16 Add Data Source Type RDBMS Name KM group Database type MySQL V Using MyISAM Source Schema Relational Mart Host martdb ensembl org Port 5316 Database JDBC URL jdbc mysql martdb ensembl org 5316 Le 5 Username anonymous Password Get Schemas vegd indrt o vega_mart_49 am E vega mart 50 C Do you want to use the existing config f vega mart 51 vega mart 52 vega mart 53 f vega mart 54 FT vega mart 55 vega mart 56 vega mart 57 f vega mart 58 vega mart 59 f 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 Helational Mart but select No when asked if you want to use the existing config Then select a t
61. me dk Add Config V Remove M List View Name Description Paste 1 Group 9 msd config msd Properties structu set GL Mart Search v Activate v Mart Form Add sub tab Sequence Converter Mart Analysis 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 GUIs 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 bios smart 36 5 12 2 MartAnalysis VIEW msd config aig VIEW XML 2 HELP 1 SeLecT DATASETS 2 RESTRICT SEARCH 0000 00000 MSD protein structures Experiment type Species name s comma separated Resolution greater than Resolution less than Assembly Class Assembly Type Go DIO mart Electron diffraction Electron microscopy Electron tomography Fibre diffraction electron Infrared spectroscopy Single crystal X ray diffraction Solid state NMR Theoretical model
62. mosome name value X gt Filter name with entrezgene value only gt Attribute name ensembl gene id Attribute name entrezgene gt lt Dataset gt lt Query gt gt lt sparql xmlns http www w3 0rg 2005 sparql results gt lt head gt lt variable name a0 gt lt variable name a1 gt lt head gt lt results gt lt result gt lt binding name a0 gt lt literal gt ENSG00000102128 lt literal gt Diosmi 92 lt binding gt binding name al literal 282808 literal lt binding gt lt result gt lt result gt lt binding name a0 gt lt Literal gt ENSG00000133169 lt literal gt lt binding gt binding name al literal 555859 literal lt binding gt lt result gt and so on lt results gt lt sparql gt 12 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 12 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 available 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
63. ng 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 Llimit 10 header 1 gt lt Dataset name 3s config Ss gt lt Attribute name s gt lt Dataset gt lt Query gt ds getName mart getConfig attr getName 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 biossgsmart 85 java BioMartSoapClient You should see some data output from the Java class 12 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 from suds client import Client client Client http localhost 9000 martsoap wsdl mart client service getMarts None 0 Oo print Using mart Ss n mart displayName ds Client service getDatasets mart name o O print Using dataset Ss n ds displayName attr client service getAttributes ds name None None 0 O print
64. ntainer guiType martform isHidden false description default displayName default name default gt lt marts gt mart conflig snp Coniig isHldden rIalse meta operation MULTISELECT description sHnp conlig displaylNarme snp config name snp config lt marts gt lt guiContainer gt lt guiContainers gt lt guiContainer gt Sample JSON Response isHidden false gurcontariners I isHidden false guiconteriners s I Jy marts isHidden false dilsplayName snp contig tooniig Sup Contig operation MULTISELECT metas M name snp config description snp contig bios smart 15 guiType martform name default displayName default description default by 1 Harts jy guiType name root displayName root description W 12 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 Smarrts Smart contlg sHp contig isHlidden Lalse meta operation MULTISELECT description snhp config displayName snp config name snp config marts Sample JSON Response bios smart 76 isHidden false displayName snp config
65. od 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 config snp config biossgsmart 80 Sample XML Response container independent false maxAttributes 0 maxContainers 0 description root displayName root name root gt lt containers gt lt container independent false maxAttributes 0 maxContainers 0 description NULL displayName Variation Information name snpsatts attribute isHidden false O O linkURL species2 Variation Summary v s valuez description displayName Variation ID name refsnp id lt attributes gt lt jattribute gt lt container gt lt containers gt lt container gt Sample JSON Response name root Containers name snpsatts displayName Variation Information description NULL maxContainers 0 maxAttributes O0 independent false attributes I name s rersnp 1d displayName Var
66. op 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 you 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 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 y Username anonymous Password Let Schemas Tables C 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 3
67. oups 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 Portal User group anonymous ES defaut RB report BI i Add Access Point M Show hidden c Name Description Source E msd config The User Management window will appear showing the current user group and users AO User Management group E ne anonymous location pee user anonymous e 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 anonymous location 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 openlD credentials in the lower left corner anonymous secure locat
68. rk 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 103
69. s 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 down 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 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 SOL 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 MartR
70. sapiens gene vega msd link description description hsapiens gene vega msd link pointedmart pointedmart msd pointedconfig hsapiens gene vega pointedconfig msd attributes attributes UniProt Swissprot Accession s e g Q6VEP3 datasets hsapiens gene vega datasets msd bio ssmart 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 eo0o0 File H Source V defaut ep Add Source F3 MSD protein struct Dataset Source Management Update L3 Mus musculus gef Link Info 3 Danio rerio genes 4 Homo sapiens ge Remove Rename Schema Editor Materialize The Link Index window will appear AO Link Index Link msd hsapiens_gene_vega link L dataset indexed msd true Cancel 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 biossgsmart 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 RRA User group anonymous e HE Start Server default p rennrt ia Rena
71. smart border lpx dotted 999 background color ddd margin Ll0px padding 5px 9 3 4 New JavaScript file Now create a JavaScript file script js with the following content bios smart 54 function initialize var queryString location search substr 1 parts queryString split amp gu parcs 0 8plit j pll Mart parts ll splrxt LL S ajax urls JIrest son guxiy Gud success function json var gui json Mart ftor var Us EE Ett kache ate d if mart name mart break j S gui append lt p gt lt strong gt GUI lt strong gt gui displayName lt p gt append p strong Number of marts lt strong gt gu ui marts length lt 7p gt S mart append p strong Mart strong mart displayName lt p gt append p strong Operation strong matt operationm lt 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 La Th CJ xX A wi Ri A G SEO http localhost 9000 myplugin gui default amp mart gene WY ur Goo Most Visited System Dashboard Bloglin
72. t 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 sql 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 f OR setOutputHandle outputHandle try QR runQuery catch InterruptedException ex Z 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 ho
73. 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 please 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 80 page language java 8 page contentType text html charset UTF 8 gt lt doctype html html lang en gt head 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 ets You can also just use a plain index html file but we will use a JSP file so we bios smart 50 can extend it later with more functionality Note
74. to 0 0 0 0 and change the http port property to the port on which you would like the non bios smart 10 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 It may take several minutes before the server starts and the site is viewable 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 DO man 11 5 Using MartConfigurator 5 1 The MartConfigurator window On first starting up the MartConfigurator window will look like this AOF MartComfgurator Versiom0 8 demo xml B Sourcel E Portal E Source V X W defaut User group anonymous Hd 7 Start Server 3 MSD Protein Structures
75. uildBot BioMart Stack Overflow BioMart MartView ReG S Most Visited System Dashboard ad G Recently Bookmarked R by exa d Tamarind Sal How Much Is Enough Welcome to Solr Federated search usi BECH wf Outline H Resize Ki Tools o Disable Cookies 4 CSS v Forms Images 1 Information CA Miscellaneous 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 SS rename Remove Paste Properties Demo v Activate Mart Search Add sub tab v My Plugin Mart Form Mart Analysis Mart Explorer Mart Wizard Restart the server and the links under the GUI container with the new type will have the correct URL i e http ocalhost 9000 myplugin 52 bios smart Gb GO GO id A Most Visited gt System Dashboard Bloglines 28264 un Employee guide BuildBot BioMart Stack Overflow BioMart MartView ReG6S T j Recently Bookmarked e R by example Grilled Tamarind Sal How Much Is Enough Welcome to Solr Federated search usi RFCAIR Disable Cookies xg CSS Forms Images v w Information L Miscellaneous 9p Outline RM Resize N Tools Your Site Title Here Not logged in Login Home Dataset summary gene vertebrates m gene WI Powered by Diossssmart 9 3 An advanced example Go back to the plugins
76. unner 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 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 bios smart 22 AAA Jobs available 1261493979561 3 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 a E 1291738800706 178 178 Job ID number Parallel threads 1 lt Update Status Time taken Started Finished Messages gt Refresh 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 corn
77. xample the following both return the response in JSON format e 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 12 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 12 3 3 Resources The following is a list of resources available from the BioMart REST API 12 3 3 1 Portal Returns the root GUI Container containing all child Containers and associated Marts URL martservice portal Method DIO 2 Mart 74 GET Parameters guitype optional Restricts returned containers to only the specified GUI type e g martform Returns Root GUI Container object Sample URL martservice portal guitype2martform Sample XML Response lt guiContainer guiType isHidden false description displayName root lt guiContainers gt name root lt guiCo
78. yname datasethidevalue master false readonly CO password SE rdf O processor S O rdfclass dino Then it must be marked which filter and attribute will be bound to the input for the dino and this is accomplished filling the function property of elements In the following example were saying that the Multiple Chromosomal Regions filter value within a query will become the sets input and the Gene Ontology attribute name will be become the annotation input for the dino bios smart 60 Ci Import from sources DP Search m Y Qo Y Hiroot Hi Choose reference dataset i DEFAULT H Y tH Ontologies _ Gene Ontology GO 3 L L HH Pathways gt Diseases gt E Hj Other species Property Value name Gene Ontology GO internalname displayname description D mart confic gene_ensembl_config_3_1 2 pointer hide default column table pointedmart pointedconfig pointeddataset pointedattribute attributelist 2ne_id goslim 3 accession linkouturl value inusers rdf datatype pointerinsource function annotation bios smart 61 C Import from sources DP Search H Ww Y Y Y Y d H3 Gene list Genomic Regions Y Y Y Y Y F wo w Y Property attribute type spliton operation datafile filterlist qualifier pointedmart pointedconfic pointeddataset pointedfilter only excluded refcontainer inusers dependson rdf required pointerinsource

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