an extensible platform for variome data integration
DESCRIPTION
WAVe talk at ITAB2010 Corfu, GreeceTRANSCRIPT
PEDRO LOPES [email protected] - Corfu, Greece
November 2nd, 2010
VARIOME DATA INTEGRATIONAN EXTENSIBLE PLATFORM FOR
WHAT IS WAVe?
http://bioinformatics.ua.pt/
‣ BACKGROUND
‣ CHALLENGES
‣ SOLUTIONS
‣ STRATEGY
‣ DEMO
‣ HIGHLIGHTS
• Applications & Resources, Features
‣ CONCLUSION
OUTLINE
‣ PERSONALIZED MEDICINE
• Custom drug design
• Improved patient specific healthcare
‣ GENOTYPE TO PHENOTYPE
• Understanding changes in our genetic sequence
‣ Causes
‣ Consequences
‣ HUMAN VARIOME
• Genome Wide Association Studies, GWAS
‣ Huge databases, huge statistics
• Locus-specific Databases, LSDBs
‣ Publish genomic variation datasets
BACKGROUND
http://bioinformatics.ua.pt/
‣ LSDB
• Independent & heterogeneous systems
‣ LOVD, UMD, MUTbase, legacy...
‣ VARIANT
• Distributed through multiple systems
• Described with distinct formats
‣ RESOURCES
• Link genomic variation datasets with original external resources
Enable agile access to integrated & enriched human variome research datasets?
CHALLENGES
http://bioinformatics.ua.pt/
‣ LSDB
• Manually curated LSDB
‣ List from HGVS
‣ VARIANT
• Web crawling engine
• LOVD API
Genes * [LSDBs + Variants + Original Resources]!
SOLUTIONS
‣ RESOURCES
• Include
‣ Original applications/content
‣ Miscellaneous data types
• Sources
‣ GeNS warehouse
‣ UniProt
http://bioinformatics.ua.pt/
‣ CORE + EXTENSIONS
Gene Variant
Disease LSDB
...
ProteinPharma Pathway
‣ HIGHLIGHTS
• Dynamic
‣ Easily extensible
‣ Update connections on-the-fly
• Original
‣ Pointers to original resources
• Centralized
‣ One-stop-shop for relevant information
STRATEGY
An extensible lightweight integration & enrichment platform for genomic variation datasets☺
http://bioinformatics.ua.pt/
DEMO | http://bioinformatics.ua.pt/WAVe
DEMO | http://bioinformatics.ua.pt/WAVe
‣ LSDB
• LOVD + MUTbase + UMD + misc legacy
‣ GENE
• GeneCards + GeneNames + Entrez
‣ PUBLICATION
• QuExT
‣ DISEASE
• OMIM
‣ PHARMACOGENOMICS
• PharmGKB
‣ LOCUS
• MapViewer + Ensembl
‣ PATHWAY
• KEGG + Reactome
‣ PROTEIN
• UniProt + PDB + Expasy + InterPro
‣ GENE ONTOLOGY
• AmiGO
HIGHLIGHT | RESOURCES
http://bioinformatics.ua.pt/
‣ LSDB
• LOVD + MUTbase + UMD + misc legacy
‣ GENE
• GeneCards + GeneNames + Entrez
‣ PUBLICATION
• QuExT
‣ DISEASE
• OMIM
‣ PHARMACOGENOMICS
• PharmGKB
‣ LOCUS
• MapViewer + Ensembl
‣ PATHWAY
• KEGG + Reactome
‣ PROTEIN
• UniProt + PDB + Expasy + InterPro
‣ GENE ONTOLOGY
• AmiGO
HIGHLIGHT | RESOURCES
~ 1350 Genes, 1550 LSDBs, 80k Variants, 100k Links!
http://bioinformatics.ua.pt/
‣ GENE SEARCH
• Direct access to genes
‣ Auto-suggest engine
• Curated genes
‣ GENE ANALYSIS WORKSPACE
• Navigation tree
‣ Holistic perspective on all data
• “Live view” mode
‣ Shows original applications/content
HIGHLIGHT | FEATURES
http://bioinformatics.ua.pt/
‣ GENE SEARCH
• Direct access to genes
‣ Auto-suggest engine
• Curated genes
‣ GENE ANALYSIS WORKSPACE
• Navigation tree
‣ Holistic perspective on all data
• “Live view” mode
‣ Shows original applications/content
HIGHLIGHT | FEATURES
‣ API
• RSS/XML access to data
‣ Usable in any framework
• Genes
‣ Access navigation tree data
‣ Google Chrome Extension
• Variants
‣ Only platform that publishes variants from multiple sources
http://bioinformatics.ua.pt/
‣ INTEGRATE
• Integrate genomic variation datasets from multiple distributed and heterogeneous sources
‣ ENRICH
• Enrich available data with connections to miscellaneous (yet relevant) resources
• Display original applications/content to maintain authorship and ownership
‣ INNOVATE
• Use “card” metaphor to provide a holistic view over human variome research
‣ ADD VALUE
• Extract and combine true added value from LSDBs
• One step forward for personalized medicine research
CONCLUSION
http://bioinformatics.ua.pt/
YOUR FEEDBACK IS HIGHLY APPRECIATED
THANK YOU!
QUESTIONS?