Clube de Gené+ca Molecular
Projecto GEN2PHEN
Uma visão holística sobre informação do genótipo ao fenótipo Pedro Lopes pedrolopes@ua.pt Universidade de Aveiro
GENOTYPE-TO-PHENOTYPE DATABASES: A HOLISTIC SOLUTION
PEDRO LOPES pedrolopes@ua.pt 14ยบ SPGH - Coimbra, Portugal November 18th, 2010
OUTLINE ‣ BACKGROUND • Summary & Objectives • Vision
‣ GEN2PHEN • Overview • LRG • LOVD • HGVbaseG2P • Knowledge Centre
‣ CONCLUSION
OBJECTIVES ‣ UNIFY
‣ ACTIVITIES
• Human and organism data
• Genotype-to-phenotype field analysis
• Genetic and genomic databases
• Development of new standards
‣ LINK • Biomedical knowledge bases ‣ Existing + New
• Creation of generic database components and services for integration • Creation of search and presentation solutions • Facilitate data exchanges • Build major GEN2PHEN portal • Deploy solutions to the community
http://www.
.org
VISION ‣ “Knowledge-Environment” • Direct mutation data submission • Seamless data integration • Holistic access to data • Community-powered
FROM INDEPENDENT G2P DATABASES TO INTELLIGENT NETWORK BIOINFORMATICS KNOWLEDGE
http://www.
.org
OVERVIEW
Exchange Formats
Café RouGE
http://www.
.org
LOCUS REFERENCE GENOMIC ‣ GOAL • Create a new standard for DNA sequence reference • Address current issues with mutation descriptions
‣ OVERVIEW • Unique stable records ‣ DNA sequence + all transcripts + conceptual translation products for variant description • Reporting structure for gene sequence variation consequences • Correlate systematic exon & amino acid numbering schemes with used legacy schemes
‣ MAINTENANCE • EBI + NCBI + GEN2PHEN
http://www.
.org
http://www.lrg-sequence.org
OVERVIEW
Exchange Formats
Café RouGE
http://www.
.org
LOVD ‣ STRATEGY • “LSDB-in-a-box”
‣ FEATURES • Web-based platform • Easy to setup and use ‣ Easy submission and curation of variants ‣ Curation tools, nomenclature checks ‣ Support for multiple genes
http://www.
.org
• Standardized data formats • Interoperability ‣ Other LSDBs ‣ Bioinformatics databases ‣ Genome browsers • UCSC
‣ Patient data
http://www.lovd.nl
OVERVIEW
Exchange Formats
Café RouGE
http://www.
.org
HGVbaseG2P ‣ OVERVIEW • Genetic association database • Integrate GWAS datasets ‣ Summary level data only ‣ Links to data sources for primary data
‣ FEATURES • Studies • Phenotypes • Browser ‣ Dataset metadata analysis
http://www.
.org
http://www.hgvbaseg2p.org
KNOWLEDGE CENTRE • Promote and explain GEN2PHEN • Distribute tools, systems and results created in the project • List upcoming GEN2PHEN meetings of interest • Host scientific debates online
• Provide direct access to available G2P data ‣ And training • Enable users feedback on available resources ‣ GEN2PHEN community • Promote (and value) data curation
http://www.
.org
http://www.gen2phen.org
CONCLUSION ‣ GENOTYPE-TO-PHENOTYPE • Key domain for personalized medicine • Efforts ‣ Molecular biologists ‣ Clinicians ‣ Bioinformaticians ‣ Developers
‣ COMMUNITY • Centre of excellence for the genotypeto-phenotype community
‣ RESOURCES • “New & Improved” ‣ Databases ‣ Tools ‣ Services ‣ Training
‣ ONGOING • Software landscape evolution • Much more to reveal until 2012
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QUESTIONS? THANK YOU!
http://bioinformatics.ua.pt/WAVe