Copyright OpenHelix. No use or reproduction without express written consent1

BioMart A query-oriented data management system developed jointly by the Ontario Institute for Cancer Research (OICR) and the European Bioinformatics Institute (EBI) Ontario Institute for Cancer Research (OICR)European Bioinformatics Institute (EBI) Materials prepared by: Mary E. Mangan, PhD Version 2.0

Copyright OpenHelix. No use or reproduction without express written consent3 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

Introduction to BioMart BioMart: Enables advanced and customized queries of data Used by data providers as a query interface or plug-in Copyright OpenHelix. No use or reproduction without express written consent4 Query these here or visit those sites Our focus: end-user interface interactions with BioMart Portal

GMOD Tools Generic Model Organism Database (GMOD) tools Many projects employ the tools, customize the look Copyright OpenHelix. No use or reproduction without express written consent5 Many projects use and contribute GMOD items

GMOD Browser vs. Query Interface GBrowse for visualization and some types of queries BioMart for generating text queries and output Copyright OpenHelix. No use or reproduction without express written consent6 wormbase.org GBrowse graphical interface wormbase.org BioMart query interface

BioMart Credits Main Team Community: offers helphttp://gmod.org/wiki/BioMart Copyright OpenHelix. No use or reproduction without express written consent7 help

Help, Documentation and Publications Main site documentation Publications and sample queries Individual sites may have additional documentation Copyright OpenHelix. No use or reproduction without express written consent8

9 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

BioMart Main Site Homepage Our main focus: Central access to data collections Copyright OpenHelix. No use or reproduction without express written consent10 Click to Portal to begin to query

Sample Query 1 From the landing page, access MARTVIEW We’ll build the sample query with this interface Copyright OpenHelix. No use or reproduction without express written consent11

Sample Query Steps: Choose Database Query will build on the left Choices will become available on the right Copyright OpenHelix. No use or reproduction without express written consent12 Query will build here Choices will be shown here

Sample Query Steps: Choose Dataset Copyright OpenHelix. No use or reproduction without express written consent13 Database: Ensembl Genes Dataset: Homo sapiens Click

Sample Query Steps: Explore Filters Copyright OpenHelix. No use or reproduction without express written consent14 Filters for Ensembl Genes Enter multiple items

Sample Query Steps: Set Gene Filter 15 IDs

Sample Query: Other Filter Options Copyright OpenHelix. No use or reproduction without express written consent16 Other filter options available

Sample Query: Attributes Indicate the items you want in your results output Copyright OpenHelix. No use or reproduction without express written consent17 Click

Sample Query: Adding Attributes Copyright OpenHelix. No use or reproduction without express written consent18

Sample Query: Output Copyright OpenHelix. No use or reproduction without express written consent19 Count for quick assessment Results for returning details Optional 2 genes

Sample Query: Results Results offer multiple display and output options Copyright OpenHelix. No use or reproduction without express written consent20 URL button output: LSCHEMANAME=default&ATTRIBUTES=hsapie ns_gene_ensembl.default.feature_page.ensembl_gene _id|hsapiens_gene_ensembl.default.feature_page.ens embl_transcript_id|hsapiens_gene_ensembl.default.fe ature_page.hgnc_symbol|hsapiens_gene_ensembl.def ault.feature_page.entrezgene|hsapiens_gene_ensembl.default.feature_page.affy_hc_g110&FILTERS=hsap iens_gene_ensembl.default.filters.ensembl_gene_id." ENSG ,ENSG "&VISIBL EPANEL=resultspanel

Copyright OpenHelix. No use or reproduction without express written consent21 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

MartService Access the BioMart data via direct server queries Script to pull the data down, or for your site or tools Copyright OpenHelix. No use or reproduction without express written consent22

Access via Web Services and Workflow Tools Galaxy Taverna and MyExperiment Copyright OpenHelix. No use or reproduction without express written consent23 Your query results in Galaxy

BioMart Plug-ins Use the BioMart data in other tools Loading Cytoscape plug-in shown Copyright OpenHelix. No use or reproduction without express written consent24

Copyright OpenHelix. No use or reproduction without express written consent25 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

BioMart Versions (0.7 and older) Sites customize the look, query options vary with the data Various versions at different sites Copyright OpenHelix. No use or reproduction without express written consent26 Site logo and navigation options often vary Query selections will build here Dataset, filters, and attributes choices will become visible here software or data version may be shown actions output help version

Samples of BioMart Sites Look and data will vary by project Main functionality will be the same Copyright OpenHelix. No use or reproduction without express written consent27

At the Database Sites find BioMart MGI, others have BioMart WormMart, Gramene Mart, HapMart Copyright OpenHelix. No use or reproduction without express written consent28

Copyright OpenHelix. No use or reproduction without express written consent29 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

BioMart Moving Forward Version 0.8 is available central.biomart.org /database/bar041 Copyright OpenHelix. No use or reproduction without express written consent30

Organization By Task and Tabs Helps to choose the type of query Can refine in many ways after first choice Copyright OpenHelix. No use or reproduction without express written consent31 Quick search Tool or task Target data Select datasets Choose filters

Example Search Sample: from publication Cancer genes from COSMIC with insertion-frameshift In Apoptosis pathway via KEGG Copyright OpenHelix. No use or reproduction without express written consent32 KEGG link Gene link COSMIC link sort

BioMart at the ICGC Site International Cancer Genome Consortium BioMart Portal interface Copyright OpenHelix. No use or reproduction without express written consent33

ICGC Query with BioMart Interface BioMart at the ICGC site Copyright OpenHelix. No use or reproduction without express written consent34

ICGC Query Results BioMart Results at ICGC site Sortable, linked, downloadable as before Copyright OpenHelix. No use or reproduction without express written consent35 sort links

Copyright OpenHelix. No use or reproduction without express written consent36 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

BioMart BioMart widely used for data management A query interface for customize and complex queries Copyright OpenHelix. No use or reproduction without express written consent37

Copyright OpenHelix. No use or reproduction without express written consent38 BioMart Worldwide Many projects employ BioMart Various versions may have different look or functionality

Copyright OpenHelix. No use or reproduction without express written consent39 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart:

Copyright OpenHelix. No use or reproduction without express written consent40