08 wp7 progresses&results-20130221

206 views
160 views

Published on

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
206
On SlideShare
0
From Embeds
0
Number of Embeds
57
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

08 wp7 progresses&results-20130221

  1. 1. WP7 Results achieved since the beginning of the project and plans for 2013
  2. 2. 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.).
  3. 3. Main achievements • Structure of Phenotypic database for peach and apple completed – Both interface and excel template
  4. 4. Main achievements • Structure of Phenotypic database for peach and apple completed – Both interface and excel template
  5. 5. Main achievements • Structure of Phenotypic database for apple completed – 8 experim. fields for peach, 7 for apple
  6. 6. Main achievements • Structure of Phenotypic database for apple completed – 1371 peach cultivars, 1746 apple cultivars
  7. 7. Main achievements • Interface to surf data – 1163 plant groups
  8. 8. Main achievements • Interface to surf data – 3470 phenotyping record
  9. 9. 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
  10. 10. Problems to be solved • Solution – Suggested method • Google refine (soon will be open refine): it helps to clean up data
  11. 11. 1 •ADDING / UPDATING SNPs SNP tool
  12. 12. 2 •UPLOADING A NEW BATCH SNP tool
  13. 13. 2 •Formatting genotypes data SNP tool
  14. 14. Genome browser and Genome mining tool • Based on GMOD • Tracks include RefSeq, gene predictions and homologous apple/peach
  15. 15. 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
  16. 16. 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
  17. 17. 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
  18. 18. DB Chado
  19. 19. 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
  20. 20. 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
  21. 21. 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
  22. 22. 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

×