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

The Plant Ontology: a tool for structural, developmental, and molecular plant biologists

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:

http://plantontology.org

Outline

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

An ontology is:

Metaphysics: The study of being or existence Knowledge sharing and reuse: The concepts of a domain and their relationships Applications: A structured vocabulary that includes definitions of concepts and relationships among them

scholarsresource.com Mason ontology, wikipedia Kyle Luckenbill, Systematic Biology

Ontologies for plant sciences:

Plant Ontology Trait Ontology Gene Ontology Chemical Entities of Biological Interest Phenotypic 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 Explicit, logical definitions and relationships among concepts

is_a

PO: storage parenchyma PO: parenchyma GO: carbohydrate storage CheBI: carbohydrate

capable_of has_parFcipant

needle = frond = vascular leaf

The PO facilitates access to and integraFon of plant genomic data

>500,000 associaFons for >1100 terms

Analyses using the PO:

I P D

is_a part_of develops_from

MEE58? AtMEE58 AtMEE58 AtMEE58 AtMEE58

hydroid xylem element

I I

plant cell plant structure axial cell whole plant

I I I

fusiform initial

MEE58? MEE58? MEE58? MEE58? D I

P

AtMEE58

The PO as a teaching tool

Tree View

Recent development of the PO

The PO now covers all plants

Seed plants Pteridophytes Bryophytes Algae New terms are being added for specific taxa.

Bowman et al, Cell, 2007

Top level re‐organizaFon of the PO

porFon of plant Fssue collecFve plant structure plant structure in vitro plant structure whole plant cardinal

• rgan part

plant organ plant cell I I P I I I I cultured cell D I P P P P I I P D

is_a part_of derives_from

GametophyFc and sporophyFc structures now described by their life cycle phase

life cycle phase plant growth and developmental stage gametophyFc phase sporophyFc phase I I I

P P

hydroid xylem element I I axial cell plant cell I plant structure I

I P

is_a participates_in

Development of machine readable text and cross‐product definiFons

Storage parenchyma: A portion of parenchyma tissue that is specialized for carbohydrate storage

is_a

PO: storage parenchyma PO: parenchyma GO: carbohydrate storage CheBI: carbohydrate

capable_of has_parFcipant

Text definitions in the genus-differentia form: Cross-product definitions that link to terms in other

• ntologies:

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