1. Copyright OpenHelix. No use or reproduction without express written consent1

2. 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 www.openhelix.com Version 2.0

3. 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: http://www.biomart.orghttp://www.biomart.org

4. Introduction to BioMart BioMart: http://www.biomart.orghttp://www.biomart.org 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

5. 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 http://www.gmod.org

6. 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

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

8. 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. 9 BioMart Agenda Introduction and Credits Basic Searches and Results Other Ways to Access Data Versions of BioMart BioMart Going Forward Summary Exercises BioMart: http://www.biomart.orghttp://www.biomart.org

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

11. 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

12. 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

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

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

15. Sample Query Steps: Set Gene Filter 15 IDs

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

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

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

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

20. Sample Query: Results Results offer multiple display and output options Copyright OpenHelix. No use or reproduction without express written consent20 URL button output: http://www.biomart.org/biomart/martview?VIRTUA 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." ENSG00000162367,ENSG00000187048"&VISIBL EPANEL=resultspanel

21. 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: http://www.biomart.orghttp://www.biomart.org

22. 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

23. Access via Web Services and Workflow Tools Galaxy Taverna and MyExperiment Copyright OpenHelix. No use or reproduction without express written consent23 http://www.usegalaxy.org Your query results in Galaxy http://www.taverna.org.uk/

24. 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

25. 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: http://www.biomart.orghttp://www.biomart.org

26. 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

27. 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

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

29. 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: http://www.biomart.orghttp://www.biomart.org

30. BioMart Moving Forward Version 0.8 is available central.biomart.org 10.1093/database/bar041 Copyright OpenHelix. No use or reproduction without express written consent30 http://central.biomart.org

31. 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

32. 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

33. BioMart at the ICGC Site International Cancer Genome Consortium BioMart Portal interface Copyright OpenHelix. No use or reproduction without express written consent33 http://icgc.org

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

35. 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

36. 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: http://www.biomart.orghttp://www.biomart.org

37. 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 http://central.biomart.org http://www.biomart.org

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

39. 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: http://www.biomart.orghttp://www.biomart.org

40. Copyright OpenHelix. No use or reproduction without express written consent40