The Plant Ontology
This presentation is the property of its rightful owner.
Sponsored Links
1 / 20

The Plant Ontology A Resource for Plant Genomics PowerPoint PPT Presentation


  • 140 Views
  • Uploaded on
  • Presentation posted in: General

The Plant Ontology A Resource for Plant Genomics. Laurel Cooper Department of Botany and Plant Pathology Oregon State University, Corvallis, OR. www.plantontology.org. The Plant Ontology - A Collaborative Effort. Cell Ontology. Ontologies for Plant Sciences:. Gene Ontology.

Download Presentation

The Plant Ontology A Resource for Plant Genomics

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


The plant ontology a resource for plant genomics

The Plant Ontology

A Resource for Plant Genomics

Laurel Cooper

Department of Botany and Plant Pathology

Oregon State University, Corvallis, OR

www.plantontology.org


The plant ontology a collaborative effort

The Plant Ontology- A Collaborative Effort

Cell Ontology


The plant ontology a resource for plant genomics

Ontologies for Plant Sciences:

Gene Ontology

Plant Ontology

Plant Trait Ontology

Chemical Entities of Biological Interest

Phenotypic QualityOntology

http://bioportal.bioontology.org/

http://www.obofoundry.org/


The plant ontology a resource for plant genomics

The Plant Ontology is…

…a controlled vocabulary

  • two aspects

  • terms cover the plant domain

  • Each term has:

  • primary name and synonyms

  • unique PO ID and url

  • definition vetted by experts, with community feedback


Organization of plant anatomy branch

Organization of Plant Anatomy Branch

is_a

  • Relations in the PO:

  • is_a andpart_ofare the backbone of all anatomical ontologies

  • has_part allows the PO to describe structural variation among taxa

is_a

New terms to describe multi-tissue plant structures released July 2012


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


Nine types of relations in the po

Nine types of Relations in the PO:


The plant ontology a resource for plant genomics

The Plant Ontology is…

…a database resource for plant science

  • Links to associations from:

  • gene expression experiments

  • EST and QTL datasets

  • mutant phenotype screens

Release #19, Dec. 2012

~2.26 million associations for 1509 PO terms covering 23 species


The plant ontology a resource for plant genomics

Collaborative development of the PO: descriptors and annotations

  • Recent Examples:

  • Oryza sativa, Japonica group -  Added ~74,000 associations based a study involving 33 laser microdissectionand 143 spatiotemporal microarrays (Aya et al, 2011. PLoS ONE 6: e261) 

  • Vitis vinifera:  Added ~ 3,400 associations to PO terms based Grapevine Expression Atlas microarray (Fasoli, et al 2012, The Plant Cell Online. doi: 10.1105/tpc.112.100230)

  • ~80 new anatomy terms for the Physcomitrella- Moss Computational Biology Resource and added ~ 82,000 new annotations to Moss genomics data (Jan 2012)

  • Addition of 1.5 million associations between Zea mays (maize) gene models and Plant Ontology terms (October 2011)


Po annotations of source tissue and growth stages

PO annotations of source tissue and growth stages

~1.5 million associations between Plant Ontology terms and ~35,000 Zea mays gene models from the sequencing of the Maize genome (Oct 2011)

Sekhon et al. (2011) Plant J 66:552-563


Browse and search for annotations on po database

Browse and Search for Annotations on PO Database


The plant ontology a resource for plant genomics

View Annotations in PO (Gene products)

Click to view the annotation details


The plant ontology a resource for plant genomics

MaizeCyc Metabolic Pathway Analysis using PO Annotations

Embryo [E]

Endosperm [D]

Embryo

Endosperm

Primary Root

Anther

Leaf

PO:0009009

PO:0009089

D 14

E12

ED2

3 AED

12 AE

EDR 1

AEDR 2

DR 2

AER1

Leaf [L]

DLR 2

3 ER

6 EDLR

DL 10

AELR 17

5 ELR

PO:0009025

26 AEDLR

2 EDL

15LR

L40

18ALR

EL11

9AEDL

(# of pathways)

A = anther (159)

E = embryo (122)

D = endosperm (106)

L = leaf (199)

R = root (145)

13 ADLR

AEL10

ADL9

AL 4

ADR2

R 23

9AR

AD1

-500 0 500

Primary Root [R]

Anther [A]

Sekhon et al. (2011) Plant J 66:552-563

PO:0020127

A 22

PO:0009066

Source: MaizeCyc project


The plant ontology a resource for plant genomics

The PO as a teaching tool: Images

Tree View


The plant ontology a resource for plant genomics

The Plant Cell branch of the PO- an example of inter-ontology cooperation

  • PO encompasses whole plant cells and references the GO definition of cell

  • Plant cell components are described by the GO cellular component ontology

  • Formerly duplicated by the Cell Type Ontology, but those have been obsoleted with a redirection to see the PO terms


Example leaf anatomy cell types

Example- Leaf Anatomy- cell types

http://en.wikipedia.org/wiki/File:Leaf_anatomy.svg


Po web services

Request terms by keyword:

…and use the real-time results† in your application

PO Web Services

Plant Ontology terms, synonyms, and definitions are now available via RESTful* web services

Detailed documentation for application developers is available on the PO web site

* REST: Representational State Transfer (an architecture for web-based data communication)† Web service results are encoded in JSON, a lightweight data-interchange format


Desktop application for annotation of image segments using ontologies aiso

Desktop Application for Annotation of Image Segments using Ontologies (AISO)

  • Sections of the images are annotated with PO terms:

  • anther

  • petal

  • sepal

  • Links out to PO database and annotations


Plant ontology consortium members and curators

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

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

Ramona L. Walls- former curator, now at iPlant


  • Login