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Haider Embrace Bosc2008
- 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)
- 9. 2. Configuration Mart Mart Mart
- 11. User Interfaces
- 14. Web Service Access <Query> <Dataset name=" hsapiens_gene_ensembl " > <Filter name=" chromosome_name " value=" 1 "/> <Attribute name=" ensembl_gene_id "/> <Attribute name=" ensembl_transcript_id "/> <Attribute name=" biotype "/> </Dataset> </Query> wget --post-data 'query= ‘ http://www.biomart.org/biomart/martservice
- 15. Web Service Access <Query> <Dataset name=" hsapiens_gene_ensembl " > <Filter name=" chromosome_name " value=" 1 "/> <Attribute name=" ensembl_gene_id "/> <Attribute name=" ensembl_transcript_id "/> <Attribute name=" biotype "/> </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."1" 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