gen2phen databases: a holistic solution
DESCRIPTION
Talk for the Molecular Genetics Club in the 14th Portuguese Human Genetics Society MeetingTRANSCRIPT
Projecto GEN2PHEN Uma visão holística sobre informaçãodo genótipo ao fenótipo
Pedro Lopes [email protected]
Universidade de Aveiro
Clube de Gené+ca Molecular
PEDRO LOPES [email protected]º SPGH - Coimbra, Portugal
November 18th, 2010
GENOTYPE-TO-PHENOTYPE DATABASES: A HOLISTIC SOLUTION
‣ BACKGROUND
• Summary & Objectives
• Vision
‣ GEN2PHEN
• Overview
• LRG
• LOVD
• HGVbaseG2P
• Knowledge Centre
‣ CONCLUSION
OUTLINE
‣ UNIFY
• Human and organism data
• Genetic and genomic databases
‣ LINK
• Biomedical knowledge bases
‣ Existing + New
‣ ACTIVITIES
• Genotype-to-phenotype field analysis
• Development of new standards
• 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
OBJECTIVES
http://www. .org
‣ “Knowledge-Environment”
• Direct mutation data submission
• Seamless data integration
• Holistic access to data
• Community-powered
VISION
FROM INDEPENDENT G2P DATABASES TO
INTELLIGENT NETWORK BIOINFORMATICS KNOWLEDGE
http://www. .org
‣ 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
LOCUS REFERENCE GENOMIC
http://www. .org
‣ 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
• Standardized data formats
• Interoperability
‣ Other LSDBs
‣ Bioinformatics databases
‣ Genome browsers
• UCSC
‣ Patient data
LOVD
http://www. .org
‣ 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
HGVbaseG2P
http://www. .org
• 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
KNOWLEDGE CENTRE
http://www. .org
‣ GENOTYPE-TO-PHENOTYPE
• Key domain for personalized medicine
• Efforts
‣ Molecular biologists
‣ Clinicians
‣ Bioinformaticians
‣ Developers
‣ COMMUNITY
• Centre of excellence for the genotype-to-phenotype community
‣ RESOURCES
• “New & Improved”
‣ Databases
‣ Tools
‣ Services
‣ Training
‣ ONGOING
• Software landscape evolution
• Much more to reveal until 2012
CONCLUSION
THANK YOU!
QUESTIONS?UP NEXT...
http://bioinformatics.ua.pt/WAVe