gen2phen databases: a holistic solution

Projecto GEN2PHEN Uma visão holística sobre informaçãodo genótipo ao fenótipo

Pedro Lopes pedrolopes@ua.pt

Universidade de Aveiro

Clube  de  Gené+ca  Molecular  

PEDRO LOPES pedrolopes@ua.pt14º 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

*

OVERVIEW

http://www. .org

Exchange Formats

Café RouGE

‣ 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

http://www.lrg-sequence.org

*

OVERVIEW

http://www. .org

Exchange Formats

Café RouGE

‣ 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

http://www.lovd.nl

*

OVERVIEW

http://www. .org

Exchange Formats

Café RouGE

‣ 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

http://www.hgvbaseg2p.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

http://www.gen2phen.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