An Extensible Platform for Variome Data Integration

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EXTENSIBLE PLATFORM FOR VARIOME DATA INTEGRATION AN

PEDRO LOPES pedrolopes@ua.pt ITAB2010 - Corfu, Greece November 2nd, 2010


PEDRO LOPES pedrolopes@ua.pt ITAB2010 - Corfu, Greece November 2nd, 2010


WHAT IS WAVe?

http://bioinformatics.ua.pt/


OUTLINE ‣ BACKGROUND

‣ DEMO

‣ CHALLENGES

‣ HIGHLIGHTS • Applications & Resources, Features

‣ SOLUTIONS ‣ CONCLUSION ‣ STRATEGY


BACKGROUND ‣ PERSONALIZED MEDICINE • Custom drug design • Improved patient specific healthcare

‣ 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!


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