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The Plant Ontology: Development of a Reference Ontology for all Plants. Plant Ontology Consortium Members and Curators *: Laurel D. Cooper*, Justin Elser , Justin Preece and Pankaj Jaiswal*: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR

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The Plant Ontology: Development of a Reference Ontology for all Plants

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The plant ontology development of a reference ontology for all plants

The Plant Ontology: Development of a Reference Ontology for all Plants

Plant Ontology Consortium Members and Curators*:

Laurel D. Cooper*, Justin Elser, Justin Preece and Pankaj Jaiswal*:

Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR

Ramona L. Walls* and Dennis W. Stevenson: The New York Botanical Garden, Bronx, NY

Maria A. Gandolfo: Department of Plant Biology, Cornell University, Ithaca, NY

Ontology Consultants:

Chris Mungall: Gene Ontology, Lawrence Berkeley National Lab, Berkeley, CA

Barry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY

www.plantontology.org


The plant ontology development of a reference ontology for all plants

Vision and Goals of the Plant Ontology:

  • Develop PO as a reference ontology for plants:

  • -describeanatomy and development ofallplants

  • Conform to OBO Foundry Principles of openness, collaborative development and interoperability, etc *

  • Facilitate annotation of comparative plant genomics data

  • Interact with other ontologies such as GO, TO, CARO, PATO, etc


The plant ontology development of a reference ontology for all plants

Challenges in expanding the Plant Ontology to cover all plants:

Diversity in anatomy, morphology, life cycles, growth patterns

Seed plants

(Angiosperms and Gymnosperms)

Pteridophytes

(Ferns and Lycopods)

Bryophytes

(Mosses, Hornworts and Liverworts)

Algae

Bowman et al, Cell, 2007


Phylogenetic diversity can result in inconsistency in nomenclature

Phylogenetic diversity can result in inconsistency in nomenclature:

Different names are used for the same structure

Different structures can have the same name e.g. ‘floret’

Instances of leaf: (PO:0025034)

maple leaf

pine needle

palm frond

Asteraceae

Poaceae

The PO provides consistent terminology for annotation of plant structures and growth and developmental stages across taxa


Recent changes to the po

Recent changes to the PO:

Two branches or subdomains of the PO are now merged:

Plant Anatomy Ontology (PAO)

PlantGrowth and Development Stage Ontology (PGDSO)


Top level of pao from caro

Top level of PAO from CARO

plant anatomical entity

portion of plant substance

plant structure

plant anatomical space

portion of plant tissue

vascular system

plant cell

plant organ

whole plant

P

H

rhizoid

collective plant structure

cardinal organ part

in vitro plant structure

ovary

collective organ part structure

embryo plant structure

trichome

H

is_a

part_of

has_part

P

H


Relations in the po allow for an accurate expression of biology

Relations in the PO allow for an accurate expression of biology

has_part allows the PO to handle structural variation among taxa

is_a andpart_ofare the backbone of all anatomical ontologies

shoot system

is_a

is_a

reproductive shoot system

develops_from describes shared developmental pathways across all taxa

flower

is_a

has_part

inflorescence

part_of

develops_from

part_of

perianth

infructescence

gynoecium


The participates in relation links an anatomical entity to a plant growth or development stage

The participates_in relation links an anatomical entity to a plant growth or development stage

whole plant growth stage

plant structure

Example:

A sporangium is_aplant organ that produces spores which participates_inasporophyte phase

plant organ

sporophyte phase

participates_in

sporangium

Describes plant structures that only occur during a specific growth and development stages

is_a


Ontology structure covers plant domain through general and specific terms

Ontology structure covers plant domain through general and specific terms

General terms for all plants, or homosporous plants

Specialized child terms for heterosporous plants, like angiosperms


How the po meets the obo foundry criteria

How the PO meets the OBO Foundry criteria:

  • Opennes- web browser, SVN, wiki

  • Common shared syntax- OBO and OWL

  • Unique identifier space: PO:xxxxxxx

  • Versioning system; #15, May 2011; etc

  • Orthogonality –yes, improving; e.g. PO-Cell Ontology

  • Textual definitions- complete


Obo foundry criteria cont

OBO Foundry criteria, Cont.

  • Relations from the OBO Relation Ontology- yes

  • Documentation- on web and publications

  • Term request tracker on SourceForge- well utilized

  • Collaborative Development-recent examples

  • Plurality of user base – wide adoption, outreach


Documentation on web and publications

Documentation- on web and publications

*Cooper and Walls, et al. The Plant Ontology: A Comparative Plant Sciences Tool for All Plant Taxa, (In preparation)

*Ilic et al, 2008. Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42.

* Avraham et al, 2008. The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations.Nucleic Acid Research, 36(Database issue):D449-D454

* Ilic et al, 2007. The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant.Plant Physiology, 2007, 143: 587-599

* Jaiswal et al, 2005. Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages.Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397


The plant ontology development of a reference ontology for all plants

Collaborative development ofthe PO:

  • Recent examples:

  • Addition of terms for Musa (bananas), Solanaceae (potatos,etc)

  • Added ~80 new terms in the recent release for the Physcomitrella (Moss)Genome Annotation group


The plant ontology development of a reference ontology for all plants

Wide range of Users and Collaborators:

Cell Ontology

Your logo could be here too!


The plant ontology facilitates comparative plant genomics

The Plant Ontology facilitates comparative plant genomics

AtMEE58

Cross-taxa comparisons:

I

>500,000+ associations for >1300 terms

MEE58?

plant cell

fusiform initial

MEE58?

AtMEE58

I

I

I

xylem element

hydroid

axial cell

MEE58?

AtMEE58

D


Annotations allow for data analysis

Annotations allow for data analysis:

Annotations may be created based on microarray, EST, QTL, protein, germplasm, phenotype or other data sets, or whole genome sequencing projects.

Example microarray data set with PO and GO annotations:

PO terms corresponding to synonyms used in the study:

* inflorescence (PO:0009049)

** shoot axis (PO:0025029)

*** whole plant in the seedling stage (PO:0000003)

  • Contact us if you are interested in providing and maintaining annotations files for your project

Data Image From: Wang, et al. (2010). The Plant Journal, 61.


Tool development

Tool Development:

PO web services being developed for the Semantic web:

Phenote annotation tool being developed for use by plant scientists


Future directions

Future directions:

  • Need to expand development of tools to link to other ontologies, e.g. GO, CL

  • Shortage of plant-specific phenotypic descriptors in PATO

  • Expanding genomics coverage of PO; e.g. TAIR, SGN, Physcomitrella, MaizeGDB and ….?

Thanks!


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