Christine Tranchant I.R.D. Montpellier

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

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

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

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

Attribut Term id TO:nnnnnnn TAIR GRAMENE IRRI MAIZEDB Ex :TO: , GO: TO : Trait ontology GO : Gene ontology GRO : Plant ontology

“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 :

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

term: grain weight (sensu Poaceae) goid: TO: 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: 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: definition_reference: www:http // trait.definition

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

<flower related trait ; TO: %fertility or sterility trait ; TO: % floret related trait ; TO: %fertility related trait ; TO: %fertility restoration trait ; TO: ; synonym:RF %female fertility restoration trait ; TO: ; synonym:FEMRF % pistil related trait ; TO: %pollen fertility ; TO: ; synonym:POFRT %incompatibility trait ; TO: %hybrid incompatibility ; TO: ; synonym:HYBIC % yield related trait ; TO: %f1-hybrid incompatibility ; TO: ; synonym:F1HYBIC %f2-generation sterility ; TO: ; synonym:F2GST %self-incompatibility ; TO: ; synonym:Genetic self-incompatibility %gametophytic incompatibility ; TO: ; synonym:GPHIC %sporophytic incompatibility ; TO: %sterility related trait ; TO: trait.ontology

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

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

Bibliographie R. Stevens, C.A. Goble and S. Bechhofer. Ontology-based Knowledge Representation for Bioinformatics. Briefings in Bioinformatics, 1(4): , November