Whole Plant Development Stages: Frequently Asked Questions

What is the purpose of an ontology for whole plant development stages?

The terms used to describe development stages in different species tend to be quite distinct, which makes comparing phenotypes and expression patterns across species difficult. Nonetheless, there are many similarities in whole plant development across species. Having a common vocabulary that links diverse species facilitates queries such as "What genes in rice and Arabidopsis are associated to the germination stage of vegetative growth?", without having to know the specific term for this stage in either species.

What happened to the old whole plant growth stage ontology?

The original "Growth Stages Ontology" was merged with the original "Development Stages Ontology" to create the "Plant Growth and Development Stage Ontology". In January 2011, the "Plant Growth and Development Stage Ontology" was merged with the "Plant Structure Ontology" to create a single "Plant Ontology". Having the two major branches of the PO in a single file makes it possible to add relationships between terms in different branches, which facilitates the creation of logical definitions and increases the reasoning power of the ontology.

Is there any way to relate species-specific whole plant development stages to this generic ontology?

The generic ontology was originally developed based on growth stages of rice, maize, Arabidopsis, Triticeae (Wheat, Oat, Barley) and soybean plants, and many of the fine-grained whole plant development stage terms remain centered on this group of species. More recently, many new or modified whole plant development stages have been added at higher levels of the ontology, making comparisons across all land plant possible. For more specific stages, the actual terms that are used by the communities working with major crop plants are represented as synonyms to generic development stage terms. For example, the term "SE.01 one node or internode visible stage" (PO:0007091) includes as synonyms these species-specific terms:
3.01 one node visible in soybean
4.02-first node detectable in barley
4.02-first node detectable in oat
4.02-first node detectable in wheat
BBCH growth stage 31
Zadok scale-31, Feekes scale-6

Why should I use these generic growth stages when there is a specific set of growth stage descriptors used by researchers working on my favorite plant?

While specific stage descriptors for a particular species allow researchers to partition development in a way that best fits that species, they do not allow for cross-species comparisons. Using the more generic growth stages in the PO makes comparisons across species possible. The Plant Ontology does not eliminate species-specific ontologies or vocabularies, rather it relates similar concepts from different vocabularies through the use of synonymy. Through the use of mapping files, a phenotype that is assigned to a species-specific stage can be associated to the more generic term within the Plant Ontology database.

How does the PO database help me find similar phenotypes in other species?

The PO database currently contains associations (annotations) for 22 species, provided by databases such as TAIR, Gramene, MaizeGDB, and plantco.de (for the species Arabidopsis thaliana, Oryza sativa, Zea mays, and Physcomitrella patens, respectively). To compare search for similar phenotypes across species, you can:

A. Query with a species-specific term and find annotations to similar stages from other species, for example germination in arabidopsis.
B. Query with a species specific term and find annotations to only a subset (one or more) of the species in PO database, for example booting stage.
C. Query with a generic term and find the specific terms (similar stages) in other species, for example fruit formation stage.
D. Query with a specific gene and find genes with similar phenotypes/expression patterns in other species, for example gene name Dwarf.

For specific information on how to use the PO-AmiGO browser to browse or search the ontology and query the database see the PO browser help document.

The whole plant development stages appear to be specific for determinate/annual species - what about perennial/indeterminate species?

The scope of the PO has been extended to cover all land plants, and many of the whole plant development stages can be used for any species. While many terms that are appropriate for determinate/annual plants persist in the PO, there are also many terms that can apply to perennial/indeterminate species. If you are interested in initiating a formal collaboration to develop the PO to accommodate a greater variety of perennial species, please contact us.

How can I participate in the development of a generic plant structure development stage ontology, so that my favorite plant is represented?

Researchers working in a plant species not currently covered by the PO ontologies are encouraged to contact the Plant Ontology Consortium. If your favorite plant has a widely accepted growth stage vocabulary that is currently in use, we will assist you in mapping your species-specific vocabulary to the generic ontology. We will collaborate to integrate species specific terms as synonyms or to broaden the scope of the generic ontology when required. The mapping file can be used by others in the field to translate species-specific terms to generic PO terms. If there is no existing species-specific ontology, the PO consortium will not create one for you, but we will assist you in finding the terms that best describe your research organism.