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Repository for the Plant Ontology
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whole plant fruit formation stage #497

Open planteome-user opened 12 years ago

planteome-user commented 12 years ago

The existing term 5 fruit formation stage (PO:0007042) is defined as "Formation of the seed-bearing structure after flowering." There are two major problems with this definition: one, it describes a process, not a stage, and two, it refers to development of a fruit, rather than to the development of a whole plant.

After reviewing the history of the PO and discussing these terms at the POC meetings on 8-14-12 and 9-4-12, we agreed that this term was originally created to describe a whole plant development stage during which fruit is being formed. We agreed to change the name and definition accordingly.

New proposed name: whole plant fruit formation stage

New proposed def.: A sporophyte reproductive stage (PO:0007130) that begins with the initiation of the first fruit (PO:0009001) of a growing season and ends with the beginning of a whole plant fruit ripening stage (PO:0007010).

Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit formation stage in its life, while a perennial may have one fruit formation stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun.

has_part fruit development stage (PO:0001002) (This could be made more specific, after we add specific types of fruit development stages.)

subset for angiosperms

As specified in the PO definition of fruit, initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then we can refer to those stages in the definition of this stage.

We expect that this definition will change slightly as we work on the new and revised terms for fruit development stages.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/497

planteome-user commented 11 years ago

Slightly modified proposed definition, with a more clearly defined beginning and end:

A sporophyte reproductive stage (PO:0007130) that begins with the initiation of the first fruit (PO:0009001) of a growing season and ends with the onset of a whole plant fruit ripening stage (PO:0007010).

Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit formation stage in its life, while a perennial may have one fruit formation stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun.

This definition will probably change slightly as we work on the new and revised terms for fruit development stages. For example, we may change definition to refer to new stages called fruit initiation stage and fruit ripening stage.

Original comment by: rlwalls2008

planteome-user commented 11 years ago

Also need to add some of the original comment to the proposed comment

Original comment: Although the use of stages like milk or particular fruit sizes properly refer to the development of an individual fruit, they are commonly used as here to extrapolate to a growth of a whole plant or a group of plants.

New proposed comment addition: Although the use of stages like milk or particular fruit sizes properly refer to the development of an individual fruit, they are used as here to extrapolate to a growth of a whole plant .

I removed the word "commonly" and took out the clause about referring to a group of plants, which is inaccurate. This definition is intended for a single plant. If users need to refer to a group of plants, they should create proper ontology definitions that refer to a population or other group of organisms.

Original comment by: rlwalls2008