Christine Tranchant I.R.D. Montpellier

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1 Christine Tranchant I.R.D. Montpellier christine.tranchant@mpl.ird.fr

2 A Resource for Comparative Grass Genomics (CSHL & Cornell University) International Rice Research Institute University of Missouri St. Louis Missouri Botanical Garden MaizeDB MIPS database The Arabidopsis Information resource Oryzabase Plant Ontology Consortium

3 But : développer un vocabulaire controlé, structuré relatif à la biologie végétale afin de décrire des ressources végétales de différentes espèces Plant Ontology Consortium Extension du paradigme de Gene Ontology

4 Plant ontology Plant ontology et Trait ontology Trait ontology (caractères phénotypiques et phénotypes) - Development stages (croissance de la plante et stades de développement) - Plant anatomy - morphologie (racine, graine, fruit, tige, feuilles etc...) - description des organes, tissus et cellules

5 Attributs du concept Terme - Term ID - Definition et references - Synonyms - Term name - Comment

6 Attribut Term id TO:nnnnnnn TAIR GRAMENE IRRI MAIZEDB Ex :TO:0000303, GO:0006818 0000001 - 0005000 0005001 - 0010000 0010001- 0015000 0015001 - 0020000 TO : Trait ontology GO : Gene ontology GRO : Plant ontology

7 “is-a relationship” “part-of relationship” “derived-from relationship” Modèle Directed acyclic graphs ou DAGs : - un terme “enfant” peut avoir plus d’un terme “parent” - un terme “enfant” peut avoir des classes de relation différentes avec ses différents parents. - trois types de relation :

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15 Format des fichiers “à plat” Deux fichiers téléchargeables : - contenant pour chaque terme la définition, l’identifiant, le commentaire, le(s) référence(s) - représentant les relations

16 term: grain weight (sensu Poaceae) goid: TO:0000509 definition: Average weights of full grain with the hull (seeds) obtained from a grass plant, representing the overall yield or produce from the field. definition_reference: GR:pj comment: This definition of the grain weight is the same as that of the seed weight (sensu Poaceae). The term was created to annotate the traits/phenpotypes, when the author does not mention about whether it is the grain or the seed, then by default the object gets annotated for this term. term: grass weed goid: TO:0000343 definition: a common grass weed Echinochloa glabbrescens or Echinochloa crus-galli (Barnyard grass), Typha spp. (Cattails), Leptochloa fascicularis (Bearded sprangletop) grows as a weed in the rice field. Can be distinguished from rice plant by the leaf shape, venation, stem cross-section and plant shape leaf shape. definition_reference: GR:pj definition_reference: ISBN:9712200299 definition_reference: www:http //www.ipm.ucdavis.edu/PMG/r682700999.html trait.definition

17 Fichier représentant les relations %term0 %term1 %term2 term1 instance de term0 mais aussi de term2 %term0 %term1 < term2 term1 instance de term0 mais aussi une partie de term2 Syntax< | % term [; db cross ref]* [; synonym:text]*[<|%term]* $ racine du graphe

18 <flower related trait ; TO:0000499 %fertility or sterility trait ; TO:0000392 % floret related trait ; TO:0000274 %fertility related trait ; TO:0000420 %fertility restoration trait ; TO:0000497 ; synonym:RF %female fertility restoration trait ; TO:0000498 ; synonym:FEMRF % pistil related trait ; TO:0000223... %pollen fertility ; TO:0000421 ; synonym:POFRT %incompatibility trait ; TO:0000035 %hybrid incompatibility ; TO:0000036 ; synonym:HYBIC % yield related trait ; TO:0000371 %f1-hybrid incompatibility ; TO:0000042 ; synonym:F1HYBIC %f2-generation sterility ; TO:0000046 ; synonym:F2GST %self-incompatibility ; TO:0000310 ; synonym:Genetic self-incompatibility %gametophytic incompatibility ; TO:0000049 ; synonym:GPHIC %sporophytic incompatibility ; TO:0000047 %sterility related trait ; TO:0000485... trait.ontology

19 Plant ontology : 231 + 476 termes Trait ontology : 595 termes Six espèces : riz, blé, mais, sorgho, orge, avoine Gene ontology En conclusion…

20 Bibliographie Gene Ontology : tool for the unification of biology. Nature Genetics, 2000, 25: 25-29 The Plant OntologyTM Consortium and Plant Ontologies Comparative and Functional Genomics, 2002, Vol 3(2), 137-142 Gramene : development and integration of trait and gene ontologies for rice Comparative and Functional Genomics, 2002, Vol 3(2), 132-136 Creating the gene ontology resource : design and implementation. Genom research, 2001, Vol 11(8), 1425-1433

21 Bibliographie R. Stevens, C.A. Goble and S. Bechhofer. Ontology-based Knowledge Representation for Bioinformatics. Briefings in Bioinformatics, 1(4):398-416, November 2000 http://www.plantontology.org http://www.gramene.org