UPDATES & FUTURE PLANS
PEDRO LOPES pedrolopes@ua.pt GEN2PHEN GAM7 - Amsterdam May 27th, 2011
GOALS ‣ INTEGRATE • Integrate genetic 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/
UPDATES ‣ USER INTERACTION • Global search + augmented browsing + tabbed browsing + custom profiles
✔done ‣ RESOURCES • All genes
✔done
• Café RouGE + LOVD-worldwide • LRG
✔done
‣ SEMANTIC WEB ✘ ongoing • Meaningful relationships ‣ Gene to Protein ≠ Gene to Variant ≠ Gene to Enzyme ≠ ...
DATA HIGHLIGHT ‣ GENES • Previously ‣ Only genes with LSDBs ‣ Lacking key genes • Update
‣ LSDB • Rebuilt LOVD API usage ‣ More variants..
‣ LRG • Added data from FTP LRG index
‣ Added information for all genes • New ‣ Gene information from Freebase
30 000 genes with 500 000 pointers!
SEARCH HIGHLIGHT ‣ GLOBAL SEARCH • Search for gene-associated IDs ‣ HGNC + OMIM + UniProt/SwissProt + KEGG + REACTOME + Ensembl + GeneOntology + GWASCentral (HGVbaseG2P) + PharmGKB
WORKSPACE HIGHLIGHT ‣ GENE NETWORK • Matches genes for previous searches
‣ TOOLBOX • LiveView Toggler
‣ OMIM:114480
• Content in new window
‣ Genes: AKT1, ATM, BRCA2, BRIP1, CASP8...
• Gene network
• Always in context
• Gene information page • Atom feed
API HIGHLIGHT ‣ API
• Genes
• Technology ‣ XML/JSON access to data • Variants ‣ Access to variant listings • http://bioinformatics.ua.pt/WAVe/variant/ COL3A1/atom
‣ Access gene-related pointers • http://bioinformatics.ua.pt/WAVe/gene/ COL3A1/json
‣ Universal Access • Load external resource within WAVe • http://bioinformatics.ua.pt/WAVe/gene/ COL3A1/uniprot:P02461
STATUS ‣ STATISTICS • Data
‣ PUBLICATIONS • ITAB2010
‣ 30 092 Genes ‣ 172 672 Variants ‣ 515 994 Pointers • 274 922 searchable (+50%)
• Version 1.3 ‣ March 2011 ‣ http://bioinformatics.ua.pt/WAVe/ status ‣ ~ 1 000 unique visitors in 1 year
‣ P Lopes and JL Oliveira An extensible platform for variome data integration 10th IEEE International Conference on Information Technology and Applications in Biomedicine Corfu, Greece, November 2010
• Human Mutation ‣ P Lopes, R Dalgleish and JL Oliveira WAVe: Web Analysis of the Variome Human Mutation, 32 March 2011 • Others...
FUTURE PLANS ‣ UNIVERSAL LSDB LIST • Integration (when available)
‣ SEMANTIC WEB • SPARQL endpoint + RDF API ‣ Share aggregated data in Semantic Web formats • Knowledge Federation ‣ Connect WAVe with external semantic applications
‣ FEEDBACK • What’s your opinion?
QUESTIONS?