Seminar Plant Genomics rd-4th-5th April 2012 Pont Royal en Provence

Transcription

1 GnpInteGr Genomique végétale Edi5on Jan Sept 2009 Coord. Delphine Steinbach, INRA URGI Versailles Total cost: 265 keuros Total grant: 74 keuros Seminar Plant Genomics rd-4th-5th April 2012 Pont Royal en Provence

2 Context: GnpIS ** Genoplante, and INRA fundings ** Maps EST, mrna (Sanger) Genome annota<on GnpMap DNA Polymorphismes GnpGenome Inter operability SIReGal Expression (microarray ) GnpProt Gene<c collec<ons, Passport data Phenotype evalua.ons (P=GxE)

3 Goal: Data integra5on to bridge gene5c and genomics data and help gene discoveries Add new tools to query GnpIS and all its databases simultenously Give users an easy access point to data : a unique simple portal To have rapidly a first synthe5c view of data, as a google search To be able to combine several datasets, to get integrated lists of results

4 Step 1: Select 3 species and exis5ng datasets Wheat Poplar Grapevine Genomic 3B pilot region - Gene annota5ons, Repeats, ISBP: F. Choulet - Physical maps: E. Paux - Gene5cs Markers, Maps: P. Leroy, P. Sourdille - QTL: J.Legouis - SNP: C. Ravel - Consor5um genome sequence and gene annota5ons: V1, V2 - Gene5c markers, maps from INRA V. Jorge, - SNP from INRA P.F. Rampant - Consor5um genome sequence and gene annota5ons: 8X, 12X - Gene5c markers, maps from INRA, Coregrapegen, A.A Blondon - SNP from INRA P. This, SnpGrapeMap

5 Step 2: Load datasets into DB, Step 3: Build links between data and tools Gene5c maps, markers, QTLs GnpIS GnpMap Wheat Naming systems! Genomic annota5ons: gene, repeats, SNPs, + markers ( mapped, + QTL mapped SNPs, Indels Genome GnpSNP Poplar Grapevine

6 Step 4: Install/configure a tool for Quick search access GnpIS ** GnpSeq GnpSNP 1) Extract Data process 2) Generate Indexes Files of indexes GnpMap Lucene ** Engine Genome Siregal 3) Query indexes with engine Ranked searches Fielded searches Merged results... ** Extension to all GnpIS database modules **Lucene technology, OpenSource hhp://lucene.apache.org/

7 First main result: GnpIS Portal Quick search tool

8 Step 5: Create a new portal to host this Quick search tool hhp://urgi.versailles.inr.fr/gnpis

9 Example: Does the DB contains my favourite marker? Where is it?

10 Marker is found on physical map, with its context, and new links to go on naviga5on

11 Example: Where is my favourite gene5c STS marker?

12 Marker found on Wheat annota5on viewer Gene ISBP SSR QTL SNP

13 Marker locus detail: name, its maps... Link to QTL

14 GnpMap: QTL details: trait, map, LG, LOD, R2 co- loc EST

15 Ex: Where is ma favourite SNP marker, QTL marker, repeat, gene, trait, kinase...

16 Second main result: Advanced query tools: Biomart Galaxy

17 Step 6: Add Biomart to create user oriented datamarts GnpIS GnpSeq 1) Extract data According User Scien<fic Ques<on Genome mart Wheat annota5on Genome mart Poplar genome- markers- snp GnpMap GnpSNP BIOMART Genome mart Marker- SNP- Genome Siregal Genome 2) Build marts 3) Query mart by sen<ng Filters 4) Get tab delimited results Genome mart Structural- func5onal annota5ons Biomart: OpenSource, Federated database system, hhp:// Provide unified access to different data sources, distributed or not geographically

18 Step 7: Add/Configure a Galaxy server (analysis workflows) hhp://urgi.versailles.inr.fr/gnpis Poster GnpAssp Poster MetaQTL Galaxy,a plamorm for interac5ve large- scale genome analysis

19 Results : Training on GnpIS Training sessions on user (lab) sites INRA GDEC Clermont- Ferrand, wheat users INRA Montpellier AGAP, grape users INRA Colmar: grape users ; INRA Bordeaux INRA Dijon: pea users Good user feedbacks, roadmaps An increase in project collabora5ons plants, fungi, trees

20 Acknowledgements - Aminah Olivia Keliet: GnpIS data integra5on: grape, poplar, wheat and Biomart - Galaxy, training - Daphné Verdelet for gene5c mapping data integra5on - Erik Kimmel: Quicksearch tool, GnpIS query interface JAVA development - Nathalie Choisne for tes5ng and promo5ng the tools for grape community and its help in training! - Michael Alaux for tes5ng and promo5ng the tools for wheat community - Joelle Amselem for tes5ng and promo5ng the tools to fungi Species Collaborators Slide 5: - Sébas5en Reboux, system administrator (for disks, CPU and backups!) - Isabelle Luyten, system database administrator - Hadi Quesneville, Hélène Lucas, Alain Charcosset for their support

21 Extra slides: - perspec5ves - URGI bioinforma5cs facility (plamorm)

22 GnpIS: Perspec5ves: New data in GnpIS : - FP7 Tri5ceaGenome, ANR 3BSeq, - ANR Muscares, ANR GrapeReseq, - ANR OakSeq - IA 2011: Breedwheat, AmaiZing ; - IA 2012: PeaMust, RapsoDyn, BioMass, Aker - IA 2012: PHENOME - EPHESIS

23 INRA URGI Facility bioinforma5cs plamorm Hardware : * Disks, * CPU + Souware + Human resources : * to manage, * to store, * to develop tools * to integrate data: * to select data, * to link data

24 URGI facility services (1) Souware development Databases, informa5on system Sequence analysis tools, pipelines Data management Inser5on, Integra5on/Interoperability Banks, Blast servers, Annota5ons Genes & repeats automa5c annota5ons (structure & func5ons) Distributed manual cura5on

25 URGI facility services (2) Souware development Databases, informa5on system Sequence analysis tools, pipelines Data management Inser5on, Integra5on/Interoperability Banks, Blast servers, Annota5ons Genes & repeats automa5c annota5ons (structure & func5ons) Distributed manual cura5on