Revision as of 19:54, 11 October 2012

POC meeting, Webex Conference Call; Date: Tuesday Oct 16th, 2012 10am PDT/1pm EDT

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POC members:

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Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-9-12?

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New fruit development stages for individual fruits

fruit development stage (PO:0001002)

def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).

comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). This stage applies to an individual fruit (PO:0009001). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.

okay

New proposed subclasses

still need to create SF tracker items and add xref to terms

fruit formation stage (PO:0025501)

Proposed def.: A fruit development stage (PO:0001002) that being with the formation of the plant zygote (PO:0000423) that is contained in that fruit and ends when its fruit ripening stage (PO:0025502) begins.

comment: A fruit formation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage applies to an individual fruit (PO:0009001). For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).

new subclasses of fruit formation stage

These are the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits. I also added a new stage for fruit initiation.

fruit initiation stage (PO:0025503): A fruit formation stage (PO:0025501) that begins with the formation of the plant zygote (PO:0000423) that is contained in that fruit (PO:0009001) and ends when the plant cells (PO:0009002) in the fruit begin to divide or expand (add GO terms).

Comment: The fruit initiation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).

What about fruits that don't grow after fertilization? I guess they go right to ripening stage? Do we need a comment to this effect? Maybe say it ends when cells start to divide or expand or senesce, if it goes directly into the ripening stage.

Note that this stage could be very brief, if fruit starts to grow or ripen right away.

We need to coordinate with go about terms like "growth".

fruit size up to 10% stage (PO:0025504): A fruit formation stage (PO:0025501) that begins after a fruit initiation stage (PO:0025503), and ends when the fruit (PO:0009001) has reached 10% of its final size.

Comment: Begins as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).

fruit size 10 to 30% stage (PO:0025505): A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.

Comment: Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).

fruit size 30 to 50% stage (PO:0025506): A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.

Comment: Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).

fruit size 50 to 70% stage (PO:0025507): A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.

Comment: Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).

fruit size 70% to final size stage (PO:0025508): A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.

Comment: Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).

fruit ripening stage

Proposed def.: A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).

Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).

Fruit development stages for whole plants

whole plant fruit development stage (PO:0025500)

New term

Continued from POC Conf. Call 10-9-12

proposed defintion: A sporophyte reproductive stage that begins when a fruit (PO:0009001) enters its fruit initiation stage (PO:0025503) on a whole plant (PO:0000003) that does not have any other fruits as part, and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

Comment: Includes whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.

whole plant fruit formation stage (PO:0007042)

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) 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 iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit development stages during its life. 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. Although the use of synonyms like 07-milk stage in rice properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.

Is it better to use whole plant fruit formation stage has_part fruit formation stage (new term, see below) or fruit formation stage part_of whole plant fruit formation stage?? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.

whole plant fruit ripening stage (PO:0007010)

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

comment: Succeeds a whole plant fruit formation stage. This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing ripening (which is a type of senescence) during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, followed by a sporophyte senescent stage (PO:0007017), as in case (1). A semelparous species may have one fruit ripening stage for each whole plant fruit developments stage (PO:0025500), followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, a plant may have multiple fruit development stages and in the sporophyte reproductive stage (PO:0007130) after all fruit has ripened, without entering dormancy or senescence, as in case (3). 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 whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of stages like dough stage properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.

Is it better to add whole plant fruit ripening stage has_part fruit ripening stage or fruit ripening stage has_part whole plant fruit ripening stage? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.

Subclasses of whole plant fruit formation stage (PO:0007042)

See SF tracker for FF.00 fruit size 10% and sibling terms

At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.

What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.