Plant Organ def'n - Githubissues

planteome-user commented 14 years ago

[Term] id: PO:0009008 name: plant organ def: "A maximal anatomical structure which is a proper part of a plant and which derives from a single ontogenetic event and includes as parts portions of tissues of at least two different types.\nExamples: stem, leaf, root." [MaizeGDB:lv] comment: Because the two or more types of tissues in an organ derive from a single ontogenetic event, organ is not a child of portion of tissue. subset: reference is_a: PO:0009011 ! plant structure

This is the definition we came up with from the POC meeting in Ithaca, Dec 17, 2009. Is everyone happy with this definition?

Reported by: cooperl09

Original Ticket: obo/plant-ontology-po-term-requests/55

planteome-user commented 14 years ago

priority: 5 --> 9

Original comment by: cooperl09

planteome-user commented 14 years ago

summary: Plant Organ definition --> Plant Organ def'n

Original comment by: cooperl09

planteome-user commented 14 years ago

I have a hard time with this definition

* What is maximal? Surely the only maximal structure is the whole plant

What is a single ontogenic event? does seed development count? In this case, again the only organ is the whole plant, which makes no sense.

I recommend the following steps:

* check everything with is_a parentage to organ right now. does everyone agree these are all intuitively organs? List some more in the gloss part of the definition. Examples are always good.

check everything that does not have is_a parentage to organ. toss out everything that is_a cell, whole organism. What's left? List some things that are not organs in the gloss part of the definition.

Should tissue and organ be disjoint classes? If so, declare them as such (so that the reasoner can find any violations - there are none right now). Tissue may be a clue to the def of organ. What is the relation between organ and tissue? Do organs have multiple tissues? Always? Is anything that is not a whole plant, cell, system or a tissue an organ?

Original comment by: cmungall

planteome-user commented 14 years ago

I agree that this definition is rather unwieldy, even though it may be technically correct. According to Merriam Webster dictionary: maximal refers to "the most complete or effective" or "being an upper limit" I am interested to hear what the others have to say.

Original comment by: cooperl09

planteome-user commented 14 years ago

Whether or not maximal is the correct term, we need some way to separate organs from parts of organs such as petiole or archegonial neck.

CARO defins organ as "Multi-tissue structure that is not part of a compound organ," but organ is a child (along with compound organ component) of "multi-tissue structure," which is defined as "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types."

I think our use of "single ontogenetic event" was meant to replace "through specific morphogenetic processes" and our use of "maximal" was meant to replace "a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types."

We may still want to consider having seperate terrms for compound organ and simple organ, because we are going to need to deal with compound organs like flowers. How do folks feel about the CARO structure of having compound organ and multi-tissue structures as parent temrs, with simple organ and compound organ part as children of multi-tissue structures?

Original comment by: rlwalls2008

planteome-user commented 14 years ago

In response to Chris's comment about distinguishing portion of tissue from organ, I think it is clear because organs must have at least two types of tissues. This much is consistent among the plant anatomy book definitions I have seen.

As to whether or not anything that is not a whole plant, cell, system or a tissue an organ, I would say no, because there are structures that are parts of organs, but not organs themselves, and layers of cells that cannot be classified as tissue (because there is only one cell type) or plant cel (because they are multiple cells), and possibly layers of tissue (although these might just be children or portion of tissue). Finally, we also have (a few) immaterial structures like pores or stomata, that will probably need a new parent term.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

Is there an organ which has only one tissue type as opposed to the minimum two defined above. Otherwise accepted.

Original comment by: jaiswalp

planteome-user commented 14 years ago

From Dennis: A flower is not compound organ because a flower is not an organ but rather an aggregate of several organs. A flower is a compound organ only if a shoot is a compound organ. A compound organ might be a fern sorus that is comprised of many sporangia with each sporangium being an organ.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

New def from 2-16-10 POC Conf call: -A plant structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.
(reworded slightly for readability)

"proper" refers to not being the whole plant Examples: stem, leaf, root

Comments: May include individual cell types that are not part of tissues. example: guard cells which are part of the leaf, idioblasts

Original comment by: cooperl09

planteome-user commented 14 years ago

priority: 9 --> 5

Original comment by: cooperl09

planteome-user commented 14 years ago

priority: 5 --> 7

Original comment by: cooperl09

planteome-user commented 14 years ago

From Dennis:

A better example of a cell that is part of an organ but not part of the tissue is an idioblast. Defintion from Esau: "cells markedly differing from other constituents of the same tissue in form, structure, or contents, from the Greek idio, peculiar".

Original comment by: rlwalls2008

planteome-user commented 14 years ago

New def from 2-16-10 POC Conf call: -A plant structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path. (reworded slightly for readability)

"proper" refers to not being the whole plant Examples: stem, leaf, root

Comments: May include individual cell types that are not part of tissues.

example: guard cells which are part of the leaf, idioblasts

FINAL

Original comment by: jaiswalp

planteome-user commented 14 years ago

I am calling this resolved and closing this item

Original comment by: cooperl09

planteome-user commented 14 years ago

status: open --> open-accepted

Original comment by: cooperl09

planteome-user commented 14 years ago

priority: 7 --> 1

Original comment by: cooperl09

planteome-user commented 14 years ago

status: open-accepted --> closed-accepted

Original comment by: cooperl09

planteome-user commented 12 years ago

I suggest we add to the comment of plant organ, to clarify that it may contain another plant organ as a part.

new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. (This is the same as the current definition, with PO ids added.)

comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094).

Original comment by: rlwalls2008

planteome-user commented 12 years ago

priority: 1 --> 5
status: closed-accepted --> closed-later

Original comment by: rlwalls2008

planteome-user commented 12 years ago

At the POC meeting on 6-19-12, we agreed to make plant organ a subtype of multi-tissue plant structure, with a slightly modified comment.

New def.: A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.

comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003).

Original comment by: rlwalls2008

planteome-user commented 12 years ago

priority: 5 --> 1
status: closed-later --> closed-fixed

Original comment by: rlwalls2008

Planteome / plant-ontology

Plant Organ def'n #55