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Talk for the 14th Portuguese Human Genetics Society annual meeting
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PEDRO LOPES [email protected].º SPGH - Coimbra, Portugal
November 18th, 2010
AN INTEGRATED VIEW FOR THE HUMAN VARIOME
PEDRO LOPES [email protected]º SPGH - Coimbra, Portugal
November 18th, 2010
‣ GENOTYPE TO PHENOTYPE
• Understanding changes in our genetic sequence
‣ Causes
‣ Consequences
‣ GEN2PHEN
• Unify human and model organism genetic variation databases
• Link biomedical knowledge
‣ GENETIC VARIATION SOFTWARE
• Genome Wide Association Studies, GWAS
‣ Huge databases, huge statistics
• Locus-specific Databases, LSDBs
‣ Publish genomic variation datasets
PREVIOUSLY...
http://bioinformatics.ua.pt/
WHAT IS WAVe?
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
WEB ANALYSIS OF THE VARIOME
http://bioinformatics.ua.pt/
‣ LSDB
• LOVD + MUTbase + UMD + misc legacy
‣ LOCUS
• GeneCards + GeneNames + Entrez
‣ PUBLICATION
• QuExT
‣ DISEASE
• OMIM
‣ PHARMACOGENOMICS
• PharmGKB
‣ GENOME
• 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
‣ API
• RSSaccess to data
• Genes
‣ Access navigation tree data
‣ Google Chrome Extension
• Variants
‣ Only platform that publishes variants from multiple sources
http://bioinformatics.ua.pt/
YOUR FEEDBACK IS HIGHLY APPRECIATED!
THANK YOU!
QUESTIONS?
