Check out the new Plant Ontology Website!
About Plant Ontology (PO)The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomy and morphology and stages of development for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics and genetics experiments.
Beginning in January 2011 (Version #14), the Plant Ontology was merged into a single ontology file (from two separate files) encompassing the following two aspects:
Plant Anatomical Entity
Botanical terms describing plant structures and other antomical entities and the relationships between them. Examples of plant anatomical entities are plant structures (PO:0009011) such as plant organ (PO:0009008), plant cell (PO:0009002), whole plant (PO:0000003), portion of plant tissue (PO:0009007), and vascular system (PO:0000034), etc.
Plant Structure Development Stage
A controlled vocabulary of terms describing the stages of plant structure development. Example of plant structure development stages are: plant tissue development stage (PO:0025423), leaf development stage (PO:0001050), whole plant development stage (PO:0007033), seed development stage (PO:0001170), and sporophyte development stage (PO:0028002), etc.
How can the PO be used?
Integrating the PO into your annotations and bioinformatics portals will facilitate cross-database queries and the comparative analysis of gene expression and phenotypes.
You can ask questions such as:
What differential set of genes regulates the development of a leaf or leaf-like structure found in angiosperms, bryophytes and gymnosperms? What phenotypes and expressed genes are common to flower development in both dicots and monocots?
To answer these questions (and many others), PO terms are being used by databases such as TAIR, NASC, Gramene, SGN and MaizeGDB to describe expression patterns of genes and the phenotypes of mutants and natural variants.
The Plant Ontology will be releasing a new, updated website in early 2014. You can preview it here. Feedback on the new site can be submitted through the Feedback/Contact Page.
New Plant Ontology Website:
Plant and Animal Genome 2014  January 11th - 15th, 2014, San Diego, CA
The PO will host a Workshop entitled Systems Biology and Ontologies on Saturday, January 11th. Presentations will cover a range of subjects from molecular networks, systems biology and their integration with ontologies to find novel insights.
Image Annotation Software Available
Annotation of Image Segments with Ontologies, v0.3 (beta)
AISO is an interactive image segmentation tool designed to allow curators to segment and annotate image data with ontology terms. Download it from the Jaiswal Lab web site Available on Linux and Mac OS X (64-bit) and Windows (32-bit).
Plant Ontology Publications:
A full list of publications can be found on our Publications Page News Archive
Participants and Contributors
The Oregon State University, New York Botanical Garden and the Cornell University are Consortium's core funded members. Collaborators and contributors include the Open Biological and Biomedical Ontologies project (OBO Foundry), the Gene Ontology Consortium (GO), the Generation Challenge Programme, SoyBase, the Solanaceae Genomics Network, the Arabidopsis Information Resource TAIR, MaizeGDB, PLEXdb, the International Rice Information System (IRIS), Oryzabase and the Moss Computational Biology Resource (COSMOSS) / (University of Freiburg).
We kindly acknowledge the Gene Ontology Consortium, all the projects using PO in their applications and all the reviewers for their valuable feedback and intellectual inputs. The core activities on ontology development, mapping to common use vocabularies, outreach and training are funded by the National Science Foundation (Award #0822201). It was previously supported by the NSF Award #0321685 to the Gramene database.
Last modified: Fri May 2 08:32:41 2014
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Plant Ontology by Plantontology.org is licensed under a Creative Commons Attribution-NoDerivs 3.0 United States License.
Based on a work at www.plantontology.org.