WP7

Results achieved since the beginning of the project and plans for 2013

Reminder of the main objectives of the WP

• To manage phenotypic data of apple and peach from the genetic materials present across EU from different locations

• To develop and utilise tools to study model traits based on functional and structural genomics

• To manage genotypic data of apple and peach for the development of a comprehensive platform including gene/QTL map position, gene ontology

• To improve collaboration on apple/peach genome studies • To speed breeding procedures (synthesis of data to select

parents; direct identification of elite individuals by markers, etc.).

Main achievements

• Structure of Phenotypic database for peach and apple completed

– Both interface and excel template

Main achievements

• Structure of Phenotypic database for peach and apple completed

– Both interface and excel template

Main achievements

• Structure of Phenotypic database for apple completed

– 8 experim. fields for peach, 7 for apple

Main achievements

• Structure of Phenotypic database for apple completed

– 1371 peach cultivars, 1746 apple cultivars

Main achievements

• Interface to surf data

– 1163 plant groups

Main achievements

• Interface to surf data

– 3470 phenotyping record

Data Standardization

• Standardization of nomenclature

– Data received on Dec 13th still lacking homogeinity

• Also language problems

• Solution

– Suggested method

• Google refine (soon will be open refine): it helps to clean up data

Problems to be solved

• Solution

– Suggested method

• Google refine (soon will be open refine): it helps to clean up data

1 •ADDING / UPDATING SNPs

SNP tool

2 •UPLOADING A NEW BATCH

SNP tool

2 •Formatting genotypes data

SNP tool

Genome browser and Genome mining tool

• Based on GMOD

• Tracks include RefSeq, gene predictions and homologous apple/peach

We are migrating the system to use a new technology suite:

• GMOD - (Generic Model Organism Database project), a collection of open source software tools for creating and managing genome-scale biological databases

• CHADO - a relational database schema linked to GMOD and capable of representing biological data such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny.

• TRIPAL - a web interface for GMOD-Chado using community supported tools.

•Currently under development

Advantages

From these new technologies we'll get:

• FLEXIBILITY - easy integration of new data (e.g. different

phenotypes; geolocalization)

• DATA GRANULARITY - data integration down to single specimen/single gene snippet

• DATA ANALYSIS - e.g. easy coupling of genotype and phenotype data

• INFRASTRUCTURE MAINTENANCE agreement with Washington State University after the project's end

Results

• Gmod+Tripal based server up and running

• complete migration of dictionary, institutions, orchards and stock data for both peach and apple datasets

• almost complete migration of phenotype data for peach

• ready to migrate apple data (as soon as we receive them...)

• knowledge base on data organization and migration on a private wiki

• reusable, data-independent migration tools

DB Chado

Problems/ToDo

• data are in Chado, could use some tuning

• Tripal web front-end need to be configured to actually show our data

• small data inconsistencies

• integration with statistical modules (?) need to be designed from scrap

Challenges for 2013

• Genotype data: – Restricted and public availability – Output format – Link to phenotype

• Re-sequencing data: – Which is the best way to make it available to partners

(public) and how to link it to the information in the database

Action Plan for 2013

WHAT WHO HOW DEADLINE

Complete uploading data in apple phenotypic db

End of March 2013

Receive genotyping infomartion Wp3 Wp4 May 2013

Receive chromosomal region (QTL) WP3, WP4, WP6 End of summer 2013

Build Genome Mining Tool in region for region of interest

End of summer 2013

Interactions between your WP and the rest of the project

• Interactions planned with other WPs of the project: – From your WP

WP2, 3, 4 web interface for data input and query and downloading

– To your WP • WP1 breeder interface questionnaire • WP2 phenotype specification • WP3 marker information, pedigree tools • WP4 phenotype, marker data • WP5 phenotype

• Interactions planned with the stakeholders of the project (and what do you expect from them?): – Breeders

• Feedback on needs for the breeder informatics tools