1. EMBRACE – BioMart Developments & Future Syed Haider Rice Group - EBI July 2008

5. In a nutshell ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG Source data (MySQL, Oracle, Postgres) DB Mart

7. 1. Transformation ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG DB Mart Source data (MySQL, Oracle, Postgres)

8. 1. Transformation MartBuilder

9. 2. Configuration Mart Mart Mart

10. 2. Configuration MartEditor

11. User Interfaces

14. Web Service Access <Query> <Dataset name=&quot; hsapiens_gene_ensembl &quot; > <Filter name=&quot; chromosome_name &quot; value=&quot; 1 &quot;/> <Attribute name=&quot; ensembl_gene_id &quot;/> <Attribute name=&quot; ensembl_transcript_id &quot;/> <Attribute name=&quot; biotype &quot;/> </Dataset> </Query> wget --post-data 'query= ‘ http://www.biomart.org/biomart/martservice

15. Web Service Access <Query> <Dataset name=&quot; hsapiens_gene_ensembl &quot; > <Filter name=&quot; chromosome_name &quot; value=&quot; 1 &quot;/> <Attribute name=&quot; ensembl_gene_id &quot;/> <Attribute name=&quot; ensembl_transcript_id &quot;/> <Attribute name=&quot; biotype &quot;/> </Dataset> </Query> wget --post-data 'query= ‘ http://www.biomart.org/biomart/martservice martview

16. VIRTUALSCHEMANAME=default &ATTRIBUTES = hsapiens_gene_ensembl .default.feature_page. ensembl_gene_id &FILTERS = hsapiens_gene_ensembl .default.filters. chromosome_name.&quot;1&quot; Web Service Access XML Free URL http://biomart.org/biomart/martview?

17. BioMart DAS Access http://www.YourBioMart.org/biomart/das/ DATASET /features? segment= FILTERS http://www.biomart.org/biomart/das/ default__hsapiens_gene_ensembl__ensembl_das_chr /features? segment= 1:1,100000 http://www.biomart.org/biomart/das/ default__hsapiens_gene_ensembl__ensembl_das_gene /features? segment= ENSG00000197194

18. Web based Access How far it has gone ?

19. Taverna

20. Bioma R t - BioConductor package

21. Cytoscape

22. Galaxy

23. Template Queries

26. Learn as you go.... Show URL Request Show XML Query Show Perl Script

30. Map Genes onto Genome

32. Map Genes onto GO GO Biological process (32) Cellular component (18) Molecular Function (24) Stem cell maintenance (7) Positive regulation of developmental process (8) Leukocyte mediated cytotoxicity (5) regulation of cell killing (12) Developmental process (15) Cell killing (17)

34. Map Genes onto Pathways Reactome Apoptosis (43) Intrinsic pathway for apoptosis (26) Signaling by Wnt (10) Signaling by TGF β (23) Activation of BH3-only proteins (5) Permeabilization of mitochondria (3) Release of apoptotic factors from mitochondria (18)

38. BioMart Central Portal – queries served