The Plant Ontology: a tool for structural, developmental, and - PowerPoint PPT Presentation

The Plant Ontology: a tool for structural, developmental, and molecular plant biologists http://plantontology.org Ramona L. Walls The New York Botanical Garden, Bronx, NY Laurel D. Cooper Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR JusBn Elser Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR Maria A. Gandolfo Department of Plant Biology, Cornell University, Ithaca, NY Chris Mungall Lawrence Berkeley NaFonal Lab, Berkeley, CA Barry Smith Department of Philosophy, University at Buffalo, NY Dennis W. Stevenson The New York Botanical Garden, Bronx, NY Pankaj Jaiswal Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR Funding:

Outline • What is an ontology? • Why use the Plant Ontology? • Recent development of the Plant Ontology

An ontology is: scholarsresource.com Mason ontology, wikipedia Kyle Luckenbill, Systematic Biology Metaphysics : The Knowledge sharing and Applications: A structured study of being or reuse: The concepts of a vocabulary that includes existence domain and their definitions of concepts and relationships relationships among them

Ontologies for plant sciences: Gene Plant Ontology Ontology Chemical Entities of Biological Interest Phenotypic Trait Ontology Attribute Ontology http://www.obofoundry.org/ http://bioportal.bioontology.org/

The PO covers plant structures and growth and developmental stage for all plants

Why use an ontology like the PO?

Plant genomic data is rapidly expanding NCBI data type # of records Genome sequences 312 Genome projects 366 Nucleotide EST 21,521,544 Nucleotide GSS 11,247,307 Nucleotide 4,164,700 Protein 1,558,053 SNP 5,418,373 Gene 351,910 Sample of genomic data available from the National Center for Biotechnology Information under the taxon Viridiplantae (green plants)

Ontologies facilitate data sharing and automated analyses through: Consistent use of vocabulary needle = frond = vascular leaf PO: is_a parenchyma CheBI: PO: storage carbohydrate parenchyma GO: carbohydrate capable_of has_parFcipant storage Explicit, logical definitions and relationships among concepts

The PO facilitates access to and integraFon of plant genomic data >500,000 associaFons for >1100 terms

Analyses using the PO: AtMEE58 MEE58? plant structure I I MEE58? AtMEE58 MEE58 ? AtMEE58 whole plant cell P plant I fusiform I initial D MEE58? AtMEE58 axial cell I is_a I I AtMEE58 MEE58? xylem part_of P hydroid element develops_from D

The PO as a teaching tool Tree View

Recent development of the PO

The PO now covers all plants Seed plants Pteridophytes Bryophytes Algae Bowman et al, Cell, 2007 New terms are being added for specific taxa.

Top level re‐organizaFon of the PO plant structure I I I I I I I whole plant P P P P in vitro plant structure collecFve plant porFon of plant organ plant cell plant Fssue structure I P D cultured cell cardinal organ part is_a I part_of P derives_from D

GametophyFc and sporophyFc structures now described by their life cycle phase life cycle plant growth and I developmental stage phase I I plant gametophyFc sporophyFc structure phase phase I plant cell P P I axial cell is_a I I I participates_in P xylem hydroid element

Development of machine readable text and cross‐product definiFons Text definitions in the genus-differentia form: Storage parenchyma: A portion of parenchyma tissue that is specialized for carbohydrate storage Cross-product definitions that link to terms in other ontologies: PO: is_a parenchyma CheBI: PO: storage carbohydrate parenchyma GO: carbohydrate capable_of has_parFcipant storage

Outreach: annotaFon workshops Custom Phenote browser allows direct annotaFon by authors

Collaborators: Contact us at: po-dev@plantontology.org http://plantontology.org http://wiki.plantontology.org