Plant Ontology Workshop Plant Biology 2004 Plant Ontology

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Plant Ontology Workshop Plant Biology 2004 Plant Ontology Consortium www. plantontology. org POC poster

Plant Ontology Workshop Plant Biology 2004 Plant Ontology Consortium www. plantontology. org POC poster #864 www. plantontology. org POC Workshop, Plant Biology 2004

Plant Ontology Workshop • Project Introduction Katica Ilic (POC project coordinator) • Development of

Plant Ontology Workshop • Project Introduction Katica Ilic (POC project coordinator) • Development of Plant Structure Ontology Pankaj Jaiswal (Gramene) • Using POC ontologies: Annotation methods and example queries Leonore Reiser (TAIR) www. plantontology. org POC Workshop, Plant Biology 2004

Plant Ontology Consortium (POC) www. plantontology. org Core participants • Cold Spring Harbor Laboratory

Plant Ontology Consortium (POC) www. plantontology. org Core participants • Cold Spring Harbor Laboratory • Cornell University • Carnegie Institution of Washington • University of Missouri at St Louis • University of Missouri - Columbia • Maize Genetics Cooperation - Stock Center Databases • Gramene • TAIR • Maize. GDB NSF Plant genome research award (2003 -2006) Collaborators Community resource (public access to POC ontologies) www. plantontology. org POC Workshop, Plant Biology 2004

Why do we need controlled vocabularies? Need Increasing need for cross-database communications Problems Heterogeneity

Why do we need controlled vocabularies? Need Increasing need for cross-database communications Problems Heterogeneity of terminology in databases Type of query: search for all the genes expressed in fruit of Arabidopsis, rice and maize Term: fruit (silique, caryopsis, kernel) Solution Unified common platform of descriptors of a ‘generic flowering plant’ Controlled vocabulary A set of standard terms used to describe a knowledge domain www. plantontology. org POC Workshop, Plant Biology 2004

What is an ontology? • A specification of a conceptualization (T. Gruber, 1993). •

What is an ontology? • A specification of a conceptualization (T. Gruber, 1993). • Formal representation of knowledge domains (Bard & Rhee, 2004). • A formal ontology is a controlled vocabulary expressed in an ontology representation language. Bio-ontology A complex hierarchical structure in which biological concepts are described by their meaning (definitions) and by their relationships to each other. Plant Ontology A set of controlled vocabulary terms that uniformly (i) ontology (i) bio-ontology describes anatomy/morphology and developmental (i) plant ontology stages of a ‘generic’ flowering plant. www. plantontology. org POC Workshop, Plant Biology 2004

The goals of the project • Develop a common set of controlled vocabularies (ontologies)

The goals of the project • Develop a common set of controlled vocabularies (ontologies) to describe anatomy/morphology and developmental stages for Arabidopsis, rice, maize and other angiosperms. • Apply this common language to describe gene expression data and phenotypes in experimentally and agronomically important plants. • Create uniform platform for plant comparative genomics (semantic framework for cross-species queries across plant databases). • Actively involve plant researchers, breeders, and systematists in development and application of vocabularies (community outreach). www. plantontology. org POC Workshop, Plant Biology 2004

Aspects of Plant Ontology has two biological domains Plant structure Terms that describe morphological/anatomical

Aspects of Plant Ontology has two biological domains Plant structure Terms that describe morphological/anatomical structures of whole plants, including organs, tissues and cell types (does not include subcellular structures). Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc. Plant growth and developmental stages Terms that describe stages in the growth and development of an entire organism, including development of individual organs, tissues and tissue systems. Examples are embryo development stages, seedling stages, flowering stages, etc. www. plantontology. org POC Workshop, Plant Biology 2004

The first release of Plant Structure Ontology • Integration of controlled vocabularies for Arabidopsis,

The first release of Plant Structure Ontology • Integration of controlled vocabularies for Arabidopsis, maize and rice • Next step, integrations of terms for legumes and Solanaceae • Currently, PO has 635 terms with definitions describing plant structure • Dynamic ontology, subject to constant changes www. plantontology. org POC Workshop, Plant Biology 2004

Plant Structure Ontology www. plantontology. org POC Workshop, Plant Biology 2004

Plant Structure Ontology www. plantontology. org POC Workshop, Plant Biology 2004

www. plantontology. org POC Workshop, Plant Biology 2004

www. plantontology. org POC Workshop, Plant Biology 2004

Community feedback What else can you do? • Suggest new terms and definitions •

Community feedback What else can you do? • Suggest new terms and definitions • Use ontology terms for describing data in your publications • If your project is generating large data sets that may require functional annotations, please contact us, we can guide you through the annotation process. E-mail: [email protected] org www. plantontology. org POC Workshop, Plant Biology 2004

Plant Ontology™ Consortium – people involved Cold Spring Harbor Laboratory Lincoln Stein, PI Doreen

Plant Ontology™ Consortium – people involved Cold Spring Harbor Laboratory Lincoln Stein, PI Doreen Ware Shuly Avram Cornell University Susan Mc. Couch Pankaj Jaiswal POC collaborators Pulien Adamse (Plant Research Int. , Pla. Net)) Richard Bruskiewich (IRRI) Roger Wise (Iowa State University) Randy Scholl (ABRC) Carnegie Inst. of Washington Sue Rhee Leonore Reiser Katica Ilic University of Missouri at St Louis Elisabeth Kellogg Peter Stevens Felipe Zapata University of Missouri-Columbia Mary Polacco Leszek Vincent Pioneer Hi-Bred International Arthur Lane Dave Selinger Monsanto Mike Edgerton Vijay Paranjape Alice Clara Augustine Maize Genetics Cooperation - Stock Center Marty Sachs NSF Plant genome research award No. 0321666 www. plantontology. org POC Workshop, Plant Biology 2004