Project Description

The main goal of the Plant Ontology (PO) project is to provide a controlled vocabulary, arranged as an ontology, for all plants, for the following plant-specific knowledge domains:

The Plant Ontology Consortium (POC) is developing an ontology that describes anatomical entities and growth and developmental stages of both flowering and non-flowering plants. The ontology is being applied to the task of annotating the spatial and temporal aspects of gene expression and observed phenotypes of mutants, natural variants and associated quantitative trait loci in a number of plant species. Annotations are being carried out in collaboration with participating plant genomics databases and large repositories of sequence datasets and seed stocks. Ontology terms developed in this project may be mapped to similar vocabularies developed by other national and international projects. In this way the PO serves as a common reference point, allowing comparative analysis of datasets. This will help to answer such questions as: "Are the expression patterns and phenotypes of orthologous genes from rice that are co-expressed during rice seed embryo development the same as those expressed in the developing embryos of maize, barley, Sorghum, and Arabidopsis or from distantly related taxa from gymnosperms or pteridophytes?" Other uses of the Plant Ontology are under development by the plant science community, including applications in ecology and systematics.

The PO is being developed according to the principles of the Open Biological Ontology (OBO) Foundry. This facilitates the interoperability of plant databases by allowing for the execution of uniform queries across databases, and allows PO terms to be used as attributes in other ontologies and applications.

The members of the POC facilitate the sharing of information and tools developed by the POC. However, each database that utilizes PO information is able to chose how it will use the information, that is, a non-federated approach to utilizing PO information is practiced.

Terminology associated with anatomy and morphology of plants may be taxon specific. Consequently, many ontologies that have been developed are species-specific. The PO aims to unite this terminology into a generic ontology that covers all plants. When necessary, taxon specific terminology is incorporated through the use of specific terms (e.g., anther wall as a child of the more general sporangium wall) and synonyms (e.g., caryopsis as a synonym for fruit).

The terms used in the PO are obtained from internationally published sources and/or requests by users. Every term in the PO is accompanied by a definition that has been vetted by a panel of experts (the curators), based on definitions from published sources. Definitions provided for terms should include a traceable source for the definition (e.g., ISBN or PMID number). If the definition has been modified, then the reference should also include a personal signature or identifier of the developer/curator/provider. Synonyms are provided wherever available. This standard contributes to an authoritative product, encouraging wide spread usage of the ontology and fostering consistency in the annotation of data by database curators.

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Data Representation:

The POC uses a simple data structure called the directed acyclic graph (DAG). This structure is a type of hierarchy where the biological concepts are organized as a network tree structure in which the nodes at the top (root) of the tree are more general cases of specific terms at the bottom (leaves) of the tree.

Like a simple hierarchy, children are not allowed to be their own ancestors; hence cycles are forbidden. Unlike a simple hierarchy, child nodes are allowed to have more than one parent node, thus allowing multiple child-to-parent relationships.

Use of term-term relationships in the plant ontology

The Plant Ontology uses the following types of relationships:

is_a
part_of
has_part
develops_from
derives_from
adjacent_to
participates_in

More information on these relations, including their definitions, is available on the PO wiki page Relations in the Plant Ontology.

Alphanumeric identifiers

Every term has a unique alphanumeric identifier, to be used as a cross-reference in collaborating databases. The terms identifiers are also associated with the ontology developers.