collective plant organ structure

[planteome-user]

Definition: A plant structure that is composed of multiple organs but is not an organ itself.

This would include structures that have multiple organs of the same type (such as the corolla) or multiple organs of different types (such as a flower), but are not themselves considered organs.

I am not clear about the distinction between a collective structure and a compound organ, especially when the structure is composed of multiple organs of the same type, such as a sorus or a gynoecium, but we do need to figure out how to deal with these structures. Right now, flower has no is_a parent.

We also need to work on the definition so that it does not include whole plant.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/63

[planteome-user]

I suggest changing the definition to one that is similar to our definition of organ, in order to distinguish collective structure from whole plant:

Definition: A plant structure that is a proper part of a plant and is composed of multiple organs but is not an organ itself.

Original comment by: rlwalls2008

[planteome-user]

Definition: A plant structure that is a proper part of a plant and is composed of multiple organs but is not an organ itself.

This works. I would add "multiple organs of the same type". This deals nicely with terms such as corolla, calyx, androeciun, etc. It does not, however, deal with terms such as flower.

Original comment by: dws409

[planteome-user]

What's a 'whorl' then. Your terms corolla, calyx, androeciun are whorls and collective organs as well. IF we go by this def then flower and corolla, calyx, androeciun will be siblings as well.

Original comment by: jaiswalp

[planteome-user]

Incfact shoot, root, inflorescence, flower, corolla, calyx, androeciun are all is_a 'collective plant structure'. So why not just leave them as it is means is_a plant structure.

Original comment by: jaiswalp

[planteome-user]

We can actually have two upper level terms to contain flower like structures. Similar tro growth stages, where certain stages were defined by bins on vegetative stage and reproductive stage. Means if a plant enters reproductive stage it is bound to bear the reproductive structures. Given this similarity, we can have the following ontology tree. It also covers your missing is_a

plant structure --is_a-- reproductive structure ------is_a--inflorescence ------is_a-- flower --is_a--vegetative structure ----is_a--shoot ------part_of--inflorescence ------part_of- flower ----is_a--root

Original comment by: jaiswalp

[planteome-user]

What Dennis and I were thinking was to have collecitve structure as the upper level term, and then vegetative shoot (or vegetative structure) and reproductive shoot (or reproductive structure) as children of collective structures. This would reduce proliferation of top level terms. However, I am certainly open to consideration of the structure you just proposed.

I do find the structure below a little odd, in that iinfloresence, which is a reproductive structure, is also part of a vegetative structure (by transitivity).

Original comment by: rlwalls2008

[planteome-user]

Chris do you have comments.

I think as long as is_a suggest that inflorescence is_a reproductive structure and found as part_of shoot which is_a vegetative structure.

Original comment by: jaiswalp

[planteome-user]

Possible defintion: A plant structure that is a proper part of a plant and is composed of two or more connected (contiguous?) plant organs.

Original comment by: rlwalls2008

[planteome-user]

New def'n: A plant structure that is a proper part of a plant and is composed of two or more organs and the associated portions of plant tissue.

POC Conf Call 3-9-10

Original comment by: cooperl09

[planteome-user]

Do embryo and seed qualify as its child? Incidentally Shoot, and stem would qualify as well.

Do we really need this term?

Original comment by: jaiswalp

[planteome-user]

Pankaj: Embryo and seed do not qualify, because they are whole plants (they do not fit the criterion of being a proper part of a plant). Yes, shoot and stem would qualify as collective plant structures. We need this term precisely so we can categorize terms like vegetative or reproductive shoot, plus terms like flower and corolla.

Original comment by: rlwalls2008

[planteome-user]

Definition agree upon at POC curators meeting on 3-9-2010: A plant structure that is a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue.

Original comment by: rlwalls2008

[planteome-user]

• status: open --> open-accepted

Original comment by: rlwalls2008

[planteome-user]

I made the folllowing terms children of collective plant structure t(they currently have no is_a parent): andreocium calyx corolla epicalyx flower gynoecium inflorescence infructenscence involucre perianth spikelet

Left all part_of relationships intact

Original comment by: rlwalls2008

[planteome-user]

• milestone: --> plant anatomy
• priority: 7 --> 1
• status: open-accepted --> closed-accepted

Original comment by: rlwalls2008

[planteome-user]

At the POC meeting on 5-8-12, it was suggested that we rename this term "collective plant organ structure", in order to make "collective plant structure" available for a more general term that includes different types of collections of plant parts.

Original comment by: rlwalls2008

[planteome-user]

• priority: 1 --> 7
• status: closed-accepted --> open-accepted

Original comment by: rlwalls2008

[planteome-user]

There can be some confusion because one plant organ can have another as a part (e.g., a sporophyll with sporangia as part, or a carpel with an ovary as part). I suggest we add a modify the definition of collective plant organs structure to make it clear that it does not encompass plant organs that have other organs as parts (add the word adjacent).

New proposed def.: A collective plant structure (PO:id) that is a proper part of a whole plant (PO:0000003) and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).

comment: A collective plant structure must have as parts at least two organs that do not have a part of relation between them, that is, one must be adjacent to the other, rather than one part of the other. The organs in a collective plant structure can be of the same type, such as a corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006) composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.

Original comment by: rlwalls2008

[planteome-user]

Just changing name of tracker item to match, so we can start new tracker for new term collective plant structure.

Original comment by: rlwalls2008

[planteome-user]

• summary: collective plant structure --> collective plant organ structure

Original comment by: rlwalls2008

[planteome-user]

Based on the discussions at POC conf call 6-12-12, we renamed this term to test:

Revised def.: A collective plant structure (PO:PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more '''adjacent'''plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).

comment: A collective plant organ structure must have as parts at least two plant organs (PO:0009008) that do not have a part_of relation between them, that is, one must be adjacent to the other, rather than one part of the other. The plant organs in a collective plant structure can be of the same type, such as the corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006), composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.

Original comment by: cooperl09

[planteome-user]

• priority: 7 --> 8
• status: open-accepted --> open

Original comment by: cooperl09

[planteome-user]

Changes to this term were accepted at the POC meeting on 6-19-12.

I also removed "collective plant organ structure" as exact synonym from PO:0025007, because it is now the primary name, and moved the Spanish and Japanese translations to collective plant structure, since they now correspond to that term.

Closing this tracker item.

Original comment by: rlwalls2008

[planteome-user]

• priority: 8 --> 1
• status: open --> closed-fixed

Original comment by: rlwalls2008

[planteome-user]

On the Feb 26, 2013 PO conf call (http://wiki.plantontology.org/index.php/POC\_Conf.\_Call\_2-26-13), we had an extended discussion about clarifying the meaning of this term for our users, in the context of the shoot system development stage terms . It was suggested to add the following to the comment: "A CPOS is a collection of plant organs (a multi-organ structure)." And that we could also add 'multi-organ structure' as a synonym.

Suggest we could add clarity by dropping the word "structure" from the name and it would not change the meaning- 'collective plant organ' is much clearer and would avoid the perceived confusion over it being a collection of "plant organ structures" (which do not exist in the ontology).

Original comment by: cooperl09

[planteome-user]

• assigned_to: rwalls --> cooperl09
• labels: 843836 --> Request: Existing term-related

Original comment by: cooperl09

[planteome-user]

This is a good solution.

Original comment by: dws409