Growth Stages Ontology FAQ
From Plant Ontology Wiki
Plant Growth Stages: Frequently Asked Questions
What is purpose of the whole plant growth stage ontology?
The terms used to describe the growth stages in different species tend to be quite distinct which makes comparing phenotypes and expression patterns across species difficult. Having a common vocabulary that links diverse species will facilitate queries such as "What genes in rice and Arabidopsis are associated to the "germination" stage of vegetative growth?" without knowing the specific term for this stage in either species.
Is there any way to relate species-specific growth stages to this generic ontology?
The generic ontology was developed based on growth stages of rice, maize, Arabidopsis, Triticeae (Wheat, Oat, Barley) and Soybean plants. The actual terms that are used by the communities working with these plants are represented as synonyms to a generic growth stage term. For example, the term "SE.01 one node or internode visible" (PO:0007091) includes as synonyms these species-specific terms namely,
"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?
The whole plant growth stage ontology does not eliminate species-specific ontologies or vocabularies, rather it relates similar concepts 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 Plant Growth Stage ontology and PO database help me find similar phenotypes in other species?
The PO database currently contains associations (annotations) to the growth stages provided by the databases TAIR and Gramene for the species Arabidopsis thaliana and rice (Oryza) respectively.
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 only a subset (one or more) of the species in PO database, for example "booting".
C. Query with a generic term and find the specific terms (similar stages) in other species, for example "fruit formation".
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 the ontologies and query the database see the PO browser help document.
The growth stages appear to be specific for determinate/annual species- what about perennial/indeterminate species?
The current scope of the project extends to some more indeterminate species such as legumes and poplar. If you are interested in initiating a formal collaboration to develop the ontologies to accommodate perennial species, please contact us.
How can I participate in the development of a generic growth 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.