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BioMart

Web Service Deployment & Programmatic Access. BioMart. Syed Haider (Rice Group) ‏ Nov’ 2008. BioMart. A Collaboration: European Bioinformatics Institute (EBI) ‏ Ontario Institute for Cancer Research (OICR) ‏. BioMart.

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BioMart

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  1. Web Service Deployment & Programmatic Access BioMart Syed Haider (Rice Group)‏ Nov’ 2008

  2. BioMart A Collaboration: • European Bioinformatics Institute (EBI)‏ • Ontario Institute for Cancer Research (OICR)‏

  3. BioMart A generic data management system with a particular focus on supporting biological research featuring: - Built-in query optimisation for fast data retrieval - Data Federation • Easy to use interfaces and APIs • Web Services and DAS

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

  5. Deploying BioMart STEP 1 - Transformation STEP 2 - Configuration

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

  7. 1. Transformation MartBuilder

  8. 2. Configuration Mart Mart Mart

  9. 2. Configuration MartEditor

  10. User Interfaces

  11. Basic Abstractions Dataset Filter Attribute

  12. Examples • of all rat genes located on chromosome 1, expressed in lungs name, chromosome, description of all mouse genes ENSMUSG00000042351 exon sequences in FASTA format

  13. MartService wget --post-data 'query= <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> ‘http://www.biomart.org/biomart/martservice

  14. MartView – XML Access wget --post-data 'query= <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> ‘http://www.biomart.org/biomart/martview

  15. MartView – URL Access VIRTUALSCHEMANAME=default &ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id &FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."1" http://biomart.org/biomart/martview?

  16. 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

  17. From MartView to MartService....

  18. Exampleget all humangeneson chromosome 1:1..10000000(bp)‏

  19. Exampleget all humangeneson chromosome 1:1..10000000(bp)‏

  20. Exampleget all humangeneson chromosome 1:1..10000000(bp)‏

  21. Exampleget all humangeneson chromosome 1:1..10000000(bp)‏

  22. Exampleget all humangeneson chromosome 1:1..10000000(bp)‏

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

  24. Practical Sessionsee tutorialsection 2.1

  25. MartService – Get Metadata 1. Get Databases/Marts www.biomart.org/biomart/martservice?type=registry Live Demo!

  26. MartService – Get Metadata 2. Get Datasets www.biomart.org/biomart/martservice? type=datasets&mart=<MART_NAME> Live Demo!

  27. MartService – Get Metadata 3. Get Attributes www.biomart.org/biomart/martservice? type=attributes&dataset=<DATASET_NAME> Live Demo!

  28. MartService – Get Metadata 4. Get Filters www.biomart.org/biomart/martservice? type=filters&dataset=<DATASET_NAME> Live Demo!

  29. Practical Sessionsee tutorialsection 3

  30. Web based AccessHow far it has gone ?

  31. Taverna

  32. BiomaRt - BioConductor package

  33. Cytoscape

  34. WebLab

  35. Galaxy

  36. Template Queries

  37. GMOD - GBrowse

  38. Credits • BioMart Team Arek Kasprzyk (OICR)‏ Junjun Zhang (OICR)‏ Syed Haider (Rice Group-EBI)‏ • Acknowledgements Benoit Ballester (Ensembl) Richard Holland (Ensembl)‏ Andreas Kahari (Ensembl) Craig Melsopp (Ensembl)‏ Bert Overduin (Ensembl) Damian Smedley (Ensembl)‏ Giulietta Spudich (Ensembl)‏ Arne Stabenau (Ensembl)‏ Phil Jones (EBI)‏ Asif Kibria (EBI) Gulam Patel (EBI)‏ Stephen Robinson (EBI)‏ Katerina Tzouvara (EBI)‏ Will Spooner (CSHL)‏ Gudmundur Thorisson (CSHL)‏ Darin London (Duke University)‏ Don Gilbert (Indiana University)‏ Steffen Durinck (NCI NIH)‏ Eric Just (Northwestern University)‏ Paul Donlon (Unilever)‏ Christina Yung (OICR)‏ Igor Antoshechkin (Caltech)‏ References Galaxy WebLab

  39. Thanks.

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