A Holistic Approach for Integrating Genomic Variation Information

PEDRO LOPES [email protected] - Torremolinos, Spain

October 28th, 2010

GENOMIC VARIATION INFORMATIONA HOLISTIC APPROACH FOR INTEGRATING

mailto:[email protected]


PEDRO LOPES [email protected] - Torremolinos, Spain

October 28th, 2010



WHAT IS WAVe?

http://bioinformatics.ua.pt/

http://bioinformatics.ua.pt/WAVe


‣ BACKGROUND

‣ CHALLENGES

‣ SOLUTIONS

‣ STRATEGY

‣ DEMO

‣ HIGHLIGHTS

• Applications & Resources, Features

‣ CONCLUSION

OUTLINE

‣ PERSONALIZED MEDICINE

• Custom drug design

• Improved patient care

‣ 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




‣ 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




‣ 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




‣ 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☺




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




‣ 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!




‣ 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




‣ 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




‣ 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




YOUR FEEDBACK IS HIGHLY APPRECIATED

THANK YOU!

QUESTIONS?

A Holistic Approach for Integrating Genomic Variation Information

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