EMBRACE – BioMart Developments & Future Syed Haider Rice Group - EBI July 2008
EMBRACE www.embracegrid.info European Model for Bioinformatics Research and Community Education <ul><li>Objective: </li></...
BioMart <ul><li>A Collaboration: </li></ul><ul><li>European Bioinformatics Institute (EBI) </li></ul><ul><li>Ontario Insti...
BioMart <ul><ul><ul><li>A generic  data management system  with a particular focus on supporting biological research featu...
In a nutshell ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG Source data (MySQL, Oracle, Po...
Deploying BioMart <ul><ul><li>STEP 1 - Transformation </li></ul></ul><ul><ul><li>STEP 2 - Configuration </li></ul></ul>
1. Transformation ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG DB Mart Source data (MySQL...
1. Transformation MartBuilder
2. Configuration Mart Mart Mart
2. Configuration MartEditor
User Interfaces
Concepts for End Users <ul><li>Dataset </li></ul><ul><li>Filter  </li></ul><ul><li>Attribute </li></ul>
Examples <ul><li>  of all rat genes </li></ul><ul><ul><li>located on chromosome 1, expressed in lungs </li></ul></ul><ul><...
Web Service Access <Query> <Dataset name=&quot; hsapiens_gene_ensembl &quot; > <Filter name=&quot; chromosome_name &quot; ...
Web Service Access <Query> <Dataset name=&quot; hsapiens_gene_ensembl &quot; > <Filter name=&quot; chromosome_name &quot; ...
VIRTUALSCHEMANAME=default &ATTRIBUTES = hsapiens_gene_ensembl .default.feature_page. ensembl_gene_id &FILTERS = hsapiens_g...
BioMart DAS Access http://www.YourBioMart.org/biomart/das/ DATASET /features? segment= FILTERS http://www.biomart.org/biom...
Web based Access How far it has gone  ?
Taverna
Bioma R t - BioConductor package
Cytoscape
Galaxy
Template Queries
 
 
Learn as you go.... Show URL Request Show XML Query Show Perl Script
<ul><li>Scalability  </li></ul><ul><ul><li>Maintaining large databases and configurations </li></ul></ul><ul><li>Security ...
<ul><li>Beyond rows and columns </li></ul><ul><ul><li>Framework for Visualisations and Analysis Tools </li></ul></ul>Future
Visualisation: Gene List Analysis & Clinical Significance <ul><li>Query </li></ul>Gene List Visualisation Gene list analys...
Map Genes onto Genome
Visualisation: Gene List Analysis & Clinical Significance <ul><li>Query </li></ul>Gene List Visualisation Gene list analys...
Map Genes onto GO GO Biological process (32) Cellular component (18) Molecular Function (24) Stem cell maintenance (7) Pos...
Visualisation: Gene List Analysis & Clinical Significance <ul><li>Query </li></ul>Gene List Visualisation Gene list analys...
Map Genes onto Pathways Reactome Apoptosis (43) Intrinsic pathway for apoptosis (26) Signaling by Wnt (10) Signaling by TG...
Future <ul><li>Summary Pages </li></ul><ul><li>Annotation for each gene </li></ul><ul><li>Entrez/Ensembl gene info </li></...
<ul><li>BioMart Team </li></ul><ul><ul><li>Arek Kasprzyk (OICR-Toronto)‏ </li></ul></ul><ul><ul><li>Syed Haider (Rice Grou...
<ul><li>Thanks. </li></ul>
BioMart Central Portal – queries served
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Haider Embrace Bosc2008

  1. 1. EMBRACE – BioMart Developments & Future Syed Haider Rice Group - EBI July 2008
  2. 2. EMBRACE www.embracegrid.info European Model for Bioinformatics Research and Community Education <ul><li>Objective: </li></ul><ul><ul><li>to integrate the major databases and software tools in bioinformatics </li></ul></ul>
  3. 3. BioMart <ul><li>A Collaboration: </li></ul><ul><li>European Bioinformatics Institute (EBI) </li></ul><ul><li>Ontario Institute for Cancer Research (OICR) </li></ul>www.biomart.org
  4. 4. BioMart <ul><ul><ul><li>A generic data management system with a particular focus on supporting biological research featuring: </li></ul></ul></ul><ul><ul><ul><li>- Built-in query optimisation for fast data retrieval </li></ul></ul></ul><ul><ul><ul><li>- Data Federation </li></ul></ul></ul><ul><ul><ul><li>Easy to use interfaces and APIs </li></ul></ul></ul><ul><ul><ul><li>Web Services and DAS </li></ul></ul></ul>
  5. 5. In a nutshell ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG Source data (MySQL, Oracle, Postgres) DB Mart
  6. 6. Deploying BioMart <ul><ul><li>STEP 1 - Transformation </li></ul></ul><ul><ul><li>STEP 2 - Configuration </li></ul></ul>
  7. 7. 1. Transformation ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG ATGCTGTTGTGC ATGCTGGACTGG ATGGCCCGATGG DB Mart Source data (MySQL, Oracle, Postgres)
  8. 8. 1. Transformation MartBuilder
  9. 9. 2. Configuration Mart Mart Mart
  10. 10. 2. Configuration MartEditor
  11. 11. User Interfaces
  12. 12. Concepts for End Users <ul><li>Dataset </li></ul><ul><li>Filter </li></ul><ul><li>Attribute </li></ul>
  13. 13. Examples <ul><li> of all rat genes </li></ul><ul><ul><li>located on chromosome 1, expressed in lungs </li></ul></ul><ul><ul><li>name, chromosome, description </li></ul></ul><ul><ul><li>of all mouse genes </li></ul></ul><ul><ul><li>ENSMUSG00000042351 </li></ul></ul><ul><ul><li>exon sequences in FASTA format </li></ul></ul><ul><ul><li>of all rat genes </li></ul></ul><ul><ul><li>up-regulated in brain and associated with a QTL for </li></ul></ul><ul><ul><li>a neurological disorder </li></ul></ul><ul><ul><li>Upstream sequences </li></ul></ul>
  14. 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. 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. 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. 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. 18. Web based Access How far it has gone ?
  19. 19. Taverna
  20. 20. Bioma R t - BioConductor package
  21. 21. Cytoscape
  22. 22. Galaxy
  23. 23. Template Queries
  24. 26. Learn as you go.... Show URL Request Show XML Query Show Perl Script
  25. 27. <ul><li>Scalability </li></ul><ul><ul><li>Maintaining large databases and configurations </li></ul></ul><ul><li>Security </li></ul><ul><ul><li>UserName/Password based access for clinical and experimental data etc </li></ul></ul><ul><li>Multiple and Custom GUIs </li></ul>Future
  26. 28. <ul><li>Beyond rows and columns </li></ul><ul><ul><li>Framework for Visualisations and Analysis Tools </li></ul></ul>Future
  27. 29. Visualisation: Gene List Analysis & Clinical Significance <ul><li>Query </li></ul>Gene List Visualisation Gene list analysis Clinical Significance
  28. 30. Map Genes onto Genome
  29. 31. Visualisation: Gene List Analysis & Clinical Significance <ul><li>Query </li></ul>Gene List Visualisation Gene list analysis Clinical Significance
  30. 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)
  31. 33. Visualisation: Gene List Analysis & Clinical Significance <ul><li>Query </li></ul>Gene List Visualisation Gene list analysis Clinical Significance
  32. 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)
  33. 35. Future <ul><li>Summary Pages </li></ul><ul><li>Annotation for each gene </li></ul><ul><li>Entrez/Ensembl gene info </li></ul><ul><li>Gene ontology/pathways </li></ul><ul><li>Biblography </li></ul><ul><li>Transcript & protein info, etc. </li></ul><ul><li>Genomic variations for each gene </li></ul><ul><li>for each cancer studied </li></ul><ul><li>Information for each patient </li></ul><ul><li>Demographics </li></ul><ul><li>History of cancer </li></ul><ul><li>Progress & outcome </li></ul><ul><li>Types of samples available </li></ul><ul><li>Histopathology of tumor </li></ul>Submission support
  34. 36. <ul><li>BioMart Team </li></ul><ul><ul><li>Arek Kasprzyk (OICR-Toronto)‏ </li></ul></ul><ul><ul><li>Syed Haider (Rice Group-EBI)‏ </li></ul></ul><ul><li>Acknowledgements </li></ul><ul><ul><li>Benoit Ballester (Ensembl) Richard Holland (Ensembl)‏ </li></ul></ul><ul><ul><li>Andreas Kahari (Ensembl) Craig Melsopp (Ensembl)‏ </li></ul></ul><ul><ul><li>Damian Smedley (Ensembl) Arne Stabenau (Ensembl)‏ </li></ul></ul><ul><ul><li>Asif Kibria (EBI) Gulam Patel (EBI)‏ </li></ul></ul><ul><ul><li>Stephen Robinson (EBI) Katerina Tzouvara (EBI)‏ </li></ul></ul><ul><ul><li>Will Spooner (CSHL) Gudmundur Thorisson (CSHL)‏ </li></ul></ul><ul><ul><li>Darin London (Duke University) Don Gilbert (Indiana University)‏ </li></ul></ul><ul><ul><li>Steffen Durinck (NCI NIH) Eric Just (Northwestern University)‏ </li></ul></ul><ul><ul><li>Paul Donlon (Unilever)‏ Christina Yung (OICR) </li></ul></ul><ul><ul><li>Igor Antoshechkin (Caltech) </li></ul></ul>Galaxy Credits References
  35. 37. <ul><li>Thanks. </li></ul>
  36. 38. BioMart Central Portal – queries served
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