GEN2PHEN Databases: A Holistic Solution

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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


UP NEXT...

QUESTIONS? THANK YOU!

http://bioinformatics.ua.pt/WAVe


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