GnpIS: an information system for plant breeding

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1 GnpIS: an information system for plant breeding 21th october 2010 Thematic day on Integrative genomics - Nantes Hadi Quesneville The URGI unit A G R I C U L T U R E A L I M E N T A T I O N E N V I R O N N E M E N T

2 URGI: Unité de Recherche en Génomique-Info Research Unit INRA unit (French National Institute for Agricultural Research) Plant breeding and Genetics Department Strong connexions with other plant INRA departments Host a Bioinformatic platform IBISA Grade Member of the French National Network of Bioinformatic Platforms (ReNaBi) Research Data integration Functional and evolutional genome dynamics The URGI unit 18/11/2010 Hadi Quesneville 2

3 Databases Central role for data analysis Repository Navigation Link heterogeneous informations Experiments: Transcriptomes, EST, SNP, chip Genome annotations: genes, repeats Genetic informations: markers, recombination rates Lineages: lines, populations, species Performance issues Adapted schema for query 18/11/2010 Hadi Quesneville 3

4 Genome data integration The URGI unit 18/11/2010 Hadi Quesneville 4

5 Data integration Data integration involves combining data residing in different sources and providing users with a unified view of these data. (from wikipedia) The URGI unit 18/11/2010 Hadi Quesneville 5

6 Genome base data integration Natural way to integrate «omics» data Map data to genome sequence Compare genome coordinates Identifiy relationships Compute correlations Few generic operations needed Generic unary and binary operators Density, counts Statistics Visualisations 2 nd Crossomics meeting 18/11/2010 Hadi Quesneville 6

7 Unary operators (1 source) range merge 18/11/2010 Hadi Quesneville 7

8 Binary operators (2 sources) overlap add 18/11/2010 Hadi Quesneville 8

9 Binary operators (2 sources) diff merge 18/11/2010 Hadi Quesneville 9

10 Inspired from R-tree (Guttman 1984) Hierarchical set of bin Adjacent bin at a level have adjacent ID Bin from different level do not overlap Coordinate indexes Assign segment to smallest bin that contain it Bins simple_feature Mb simple_feature_id int kb seq_region_id int kb bin float kb seq_region_start int seq_region_end int Chromosome seq_region_strand analysis_id tinyint int score double 18/11/2010 Hadi Quesneville 10

11 Coordinate indexes Mb 100kb 10kb 1kb Bins Chromosome simple_feature Select * from simple_feature where seq_region_id=1 AND ( bin = OR bin = Bin level ( x10 l ) Bin number ( / 10 l ) OR bin between and OR bin between and ) simple_feature_id seq_region_id bin seq_region_start seq_region_end seq_region_strand analysis_id score int int float int int tinyint int double AND seq_region_start<= AND seq_region_end >= /11/2010 Hadi Quesneville 11

12 S-MART The URGI unit Hadi Quesneville

13 Database data integration The URGI unit 18/11/2010 Hadi Quesneville 13

14 Architectures Data integration is defined as a triple <G,S,M> where: G is the global (or mediated) schema, S is the heterogeneous set of source schemas, M is the mapping that maps queries between the source and the global schemas. (from wikipedia) Two architectures Data Warehouse Virtual Database 2 nd Crossomics meeting 18/11/2010 Hadi Quesneville 14

15 GnpMap GnpIS data warehouse EST, mrna Maps DNA Polymorphismes Genome annotation GnpGenomeAster SIReGal Genetic collections Transcriptome Proteome GnpProt Phenotype evaluations (P=GxE) The URGI unit 18/11/2010 Hadi Quesneville 15

16 Data consistency GnpGenome foreign keys GnpIS Xref GnpSNP A foreign key is a relationship or link between two tables which ensures that the data stored in a database is consistent. GnpArray GnpProt Deleting a record that contains a value referred to by a foreign key in another table would break referential integrity. GnpMap SIReGal Some relational database management systems (RDBMS) can enforce referential integrity GnpSeq Aster Core module Ephesis by deleting the foreign key rows as well to maintain integrity, by returning an error and not performing the delete. Architecturally, this offers a tightly coupled approach because the data reside together in a single repository at query-time The URGI unit 18/11/2010 Hadi Quesneville 16

17 Interoperability A property referring to the ability of diverse systems to work together (inter-operate) capability of different programs to exchange data via a common set of exchange formats, to read and write the same file formats, and to use the same protocols. (loose) links between RDBMS Xrefs Web services Tools over the data warehouse Quick search Biomart Galaxy (from wikipedia) 2 nd Crossomics meeting 18/11/2010 Hadi Quesneville 17

18 GnpIS interoperability Submission Queries Pipelines DB Data Mart Web Interfaces submission Complex queries Excel Files Simple queries The URGI unit 18/11/2010 Hadi Quesneville 18

19 Quick search The URGI unit 18/11/2010 Hadi Quesneville 19

20 Quick search results The URGI unit 18/11/2010 Hadi Quesneville 20

21 Biomart: advanced search The URGI unit 18/11/2010 Hadi Quesneville 21

22 Get QTL by theme, trait, QTL name, markers. Hadi Quesneville

23 Attributes for results Hadi Quesneville

24 Results and links for details Delphine Steinbach Hadi Quesneville

25 Interoperability (QTL) with GnpMap GnpGenome Poplar GnpMap URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 25

26 ( markers QTL mapped on GnpGenome (via URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 26

27 QTLs found in GnpMap URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 27

28 A data integration workbench The URGI unit 18/11/2010 Hadi Quesneville 28

29 Galaxy URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 29

30 Get data from Biomart URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 30

31 Text manipulation Exemple: URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 31

32 Other manipulations URGI Démo GnpIS Dijon Hadi Quesneville 20/05/10 32

33 Galaxy Workflow The URGI unit 18/11/2010 Hadi Quesneville 33

34 URGI - Data Integration Workbench GnpIS External DB Data Mart Data Mart Data banks User files Galaxy Developer Pipelines User The URGI unit 18/11/2010 Hadi Quesneville 34

35 Acknowlegments URGI M. Alaux, F. Alfama, J. Amselem, N. Choisne, S. Durand, O. Inizan, V. Jamilloux, A. Keliet, E. Kimmel, N. Lapalu, I. Luyten, N. Mohellibi, C. Pommier, H. Quesneville, S. Reboux, D. Steinbach, M. Zytnicki S. Arnoux (CDD), M. Bras (CDD), B. Brault (CDD), L. Brigitte (CDD), T. Flutre (PhD), C. Hoede (CDD), H. Mors (Master2) E. Permal (Post-doc), D. Verdelet (CDD), D.Valdenaire (CDD) left URGI B. Hilseberger (CDD) The URGI unit 09/11/09 Hadi Quesneville

36 Partners Wheat genomics: P. Leroy, C. Ravel, E. Paux, C. Feuillet Grape genomics A.F. Adam-Blondon, M. Moroldo SNP thematic D. Brunel, F. Granier, H. McKhann C. De Poittevin Genetic resources J.M. Prosperi, P. Roumet Fungi genomics M.H. Lebrun, T. Rouxel Maize genomics M. Falque, J. Joets, A. Charcosset Colot s Lab V. Colot, I. Ahmed, A. Sarazin Tree genomics C.Plomion, C. Poittevin The URGI unit 18/11/2010 Hadi Quesneville 36

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