HOLISTIC APPROACH FOR INTEGRATING GENOMIC VARIATION INFORMATION A
PEDRO LOPES pedrolopes@ua.pt JBI2010 - Torremolinos, Spain October 28th, 2010
PEDRO LOPES pedrolopes@ua.pt JBI2010 - Torremolinos, Spain October 28th, 2010
WHAT IS WAVe?
http://bioinformatics.ua.pt/
OUTLINE ‣ BACKGROUND ‣ CHALLENGES ‣ SOLUTIONS ‣ STRATEGY ‣ DEMO ‣ HIGHLIGHTS • Applications & Resources, Features
‣ CONCLUSION
BACKGROUND ‣ PERSONALIZED MEDICINE • Custom drug design • Improved patient care
‣ HUMAN VARIOME • Genome Wide Association Studies, GWAS ‣ Huge databases, huge statistics • Locus-specific Databases, LSDBs ‣ Publish genomic variation datasets
‣ GENOTYPE TO PHENOTYPE • Understanding changes in our genetic sequence ‣ Causes ‣ Consequences
http://bioinformatics.ua.pt/
CHALLENGES Enable agile access to integrated & enriched human variome research datasets
? ‣ LSDB
• Independent & heterogeneous systems ‣ LOVD, UMD, MUTbase, legacy...
‣ VARIANT • Distributed through multiple systems • Described with distinct formats
http://bioinformatics.ua.pt/
‣ RESOURCES • Link genomic variation datasets with original external resources
SOLUTIONS
!
Genes * [LSDBs + Variants + Original Resources]
‣ LSDB • Manually curated LSDB ‣ List from HGVS
‣ RESOURCES • Include ‣ Original applications/content ‣ Miscellaneous data types
‣ VARIANT
• Sources
• Web crawling engine
‣ GeNS warehouse
• LOVD API
‣ UniProt
http://bioinformatics.ua.pt/
STRATEGY
☺
An extensible lightweight integration & enrichment platform for genomic variation datasets
‣ CORE + EXTENSIONS
‣ HIGHLIGHTS • Dynamic ‣ Easily extensible
Disease ...
Protein
Gene
Pharma
LSDB
‣ Update connections on-the-fly Variant Pathway
• Original ‣ Pointers to original resources • Centralized ‣ One-stop-shop for relevant information
http://bioinformatics.ua.pt/
DEMO | http://bioinformatics.ua.pt/WAVe
DEMO | http://bioinformatics.ua.pt/WAVe
HIGHLIGHT | RESOURCES ‣ 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
http://bioinformatics.ua.pt/
HIGHLIGHT | RESOURCES ‣ LSDB • LOVD + MUTbase + UMD + misc legacy
‣ GENE • GeneCards + GeneNames + Entrez
‣ PHARMACOGENOMICS • PharmGKB
‣ LOCUS • MapViewer + Ensembl
‣ PUBLICATION
‣ PATHWAY
‣ DISEASE
‣ PROTEIN
~ 1350 Genes, 1550 LSDBs, 80k Variants, 100k Links ! • QuExT • KEGG + Reactome • OMIM
• UniProt + PDB + Expasy + InterPro
‣ GENE ONTOLOGY • AmiGO
http://bioinformatics.ua.pt/
HIGHLIGHT | FEATURES ‣ 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
http://bioinformatics.ua.pt/
HIGHLIGHT | FEATURES ‣ GENE SEARCH • Direct access to genes ‣ Auto-suggest engine • Curated genes
‣ API • RSS/XML access to data ‣ Usable in any framework • Genes ‣ Access navigation tree data
‣ GENE ANALYSIS WORKSPACE • Navigation tree ‣ Holistic perspective on all data • “Live view” mode ‣ Shows original applications/content
http://bioinformatics.ua.pt/
‣ Google Chrome Extension • Variants ‣ Only platform that publishes variants from multiple sources
CONCLUSION ‣ 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
http://bioinformatics.ua.pt/
YOUR FEEDBACK IS HIGHLY APPRECIATED QUESTIONS? THANK YOU!