Title: Biomart 2007 Author: Arek Kasprzyk

1. BioMart 2007 Arek Kasprzyk European Bioinformatics Institute BOSC Vienna, July 2007

2. Data Flow Mart JAVA PERL Source data DAS Web GUI Command line Desktop GUI Web Service

3. Data Flow JAVA PERL Mart DAS Web GUI Command line Desktop GUI Web Service

4. Admin Tools

6. Data Flow Mart JAVA PERL Source data DAS Web GUI Command line Desktop GUI Web Service

7. MartBuilder

8. MartBuilder

9. MartBuilder

10. MartView

11. API my $initializer = BioMart::Initializer->new('registryFile'=>$confFile); my $registry = $initializer->getRegistry; my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>’central_server_1'); $query->setDataset(" hsapiens_gene_ensembl "); $query->addFilter(" chromosome_name ", [” 1 "]); $query->addAttribute(" ensembl_gene_id "); $query->addAttribute(" ensembl_transcript_id "); $query->addAttribute(” ensembl_peptide_id "); $query->setDataset(“ msd ”); $query->addFilter(” experiment_type ", [” NMR "]); $query->addAttribute(" pdb_id "); $query->addAttribute(” resolution "); $query->addAttribute(” release_date "); $query->addAttribute(” header "); my $query_runner = BioMart::QueryRunner->new(); $query_runner->execute($query); $query_runner->printResults();

12. Web service <Query virtualSchemaName=&quot;central_server_1&quot;> <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; ensembl_peptide_id &quot;/> </Dataset> <Dataset name=&quot; msd &quot;> <Filter name=&quot; experiment_type &quot; value=” NMR &quot;/> <Attribute name=&quot; pdb_id &quot;/> <Attribute name=” resolution &quot;/> <Attribute name=” release_date &quot;/> <Attribute name=” header &quot;/> </Dataset> </Query>

15. Query -O 5utr.dat <?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?> <!DOCTYPE Query> <Query virtualSchemaName = &quot;default&quot; count = &quot;&quot; softwareVersion = &quot;0.5&quot; > <Dataset name=&quot; hsapiens_gene_ensembl &quot; > <Attribute name=&quot; ensembl_gene_id &quot;/> <Attribute name=&quot; ensembl_transcript_id &quot;/> <Filter name=&quot; chromosome_name &quot; value=&quot; 1 &quot;/> <Filter name=&quot; band_end &quot; value=” p36.33 &quot; / > <Filter name=&quot; band_start &quot; value=” q44 &quot;/> </Dataset> <Dataset name=&quot; msd &quot;> <Attribute name=&quot; pdb_id &quot;/> <Attribute name=” experiment_type &quot;/> <Filter name=&quot; experiment_type &quot; value=” NMR &quot;/> </Dataset> </Query> wget -q 'http://www.biomart.org/biomart/martservice?query=

17. Genomic data

18. Uniprot, MSD, ArrayExpress

19. Model organism databases

20. Developmental models

21. Proteomics

22. Name Fragment Position Alleles strand SNP1 AL139258 1659852 T/A 1 SNP2 NT_25698 2569873 C/T -1 SNP3 chr13 1125698 C/G 1 Genetics of Infectious and Autoimmune Diseases, Pasteur Institute, INSERM U730, Paris, France. Target SNP selection for the study of type 1 diabetes (T1D), malaria and dengue Data conversion and integration Ensembl HapMap NCBI UCSC Priopriatery data Diabetes-Gene Association DataBase Combined proprietary and public data

23. CAPRISA understanding HIV pathogenesis and epidemiology as well as HIV/AIDS treatment and prevention Clinical Data MID Cellular Immunity Humoral Immunity HLA Typing Sequence & Sequence Related Pipeline

26. 1. Filter 2. Attributes 3. Results Use Example 1 All genes in the human genome up-regulated in Pancreatic Adenocarcinomas (PDACs) vs Normal Pancreas (ND))

27. 1. Filter 2. Attributes 3. Results Use Example 2 all upstream sequences for all genes on chromosome 1 up-regulated in Pancreatic Adenocarcinomas (PDACs) vs Normal Pancreas (ND))

28. 1. Filter 2. Attributes Use Example 3 3. Results Just Finished my experiment and would like to get the overlaps between my results and those reported in previous studies !

29. Web service

30. Perl

31. DAS

32. Bioconductor package biomaRt

33. Galaxy

34. Taverna

35. Central Server (www.biomart.org)

36. www.biomart.org/biomart/ martservice

37. Future plans

42. New GUI framework Gene Id conversion Functional annotation Compare two gene lists Analyze gene list Draw distribution Full search Draw bla bla chart Home Welcome to my data mining website SITE HEADER

43. New GUI framework Gene Id conversion Functional annotation Compare two gene lists Analyze gene list Genbank Trembl Uniprot Submit Draw distribution Full search paste your ids here Draw bla bla chart Hugo Home SITE HEADER

44. New GUI framework Home Gene Id converter Fu Full search Welcome to my data mining website

45. New GUI framework Hugo Genebank Uniprot Swissprot Submit paste your ids here Home Fu Full search Gene Id conversion

46. Cytogenetic distribution of pancreatic cancer genes satisfying my query (histogram)

47. Cytogenetic distribution of pancreatic cancer genes satisfying my query (ideogram)

48. Cytogenetic distribution of chromosomal aberrations in pancreatic cancer

50. New GUI framework

51. New GUI framework