multi-tissue plant structure

[planteome-user]

We currently have several plant structures that cannot be classified (ovary, seed funicle, arilloid, fruit distal end), and so need to be direct subclasses of plant structure. One way to classify them would be to add a term for multi-tissue structure, loosely following CARO.

This would be parent to plant organs, collective plant structures, cardinal organ parts, and those weird, unclassifiable things like arilloid or ovary.

CARO:multi-tissue structure: 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. -- Examples are simple organ and compound organ component.

The CARO term is problematic for PO, because we may not want to restrict our class to structures with bona-fide boundaries.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/480

[planteome-user]

proposed definition: A plant structure that has as parts two or more portions of plant tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit.

Comment: maybe give some examples

Original comment by: rlwalls2008

[planteome-user]

didn't we agree to use 'organ' for these.

Original comment by: jaiswalp

[planteome-user]

You are right that the definition I proposed (based on CARO's definition) is pretty much the same as the definition of plant organ. What I had in mind was something more broad -- a class that could include not only organs, but also cardinal organ parts, collective plant structures, and other structures that have more than two tissues but can't be classified in any of our existing categories. Maybe we need to change the wording from "distinct structural unit" to something more broad. The other option is just do what we are doing now, and keep the oddballs as subtypes of plant structure. The number of oddballs keeps growing, though.

Original comment by: rlwalls2008

[planteome-user]

seed funicle is the funiculus, which is a part of an ovule. It is the funiculus of a mature ovule. It is the the only funicle (funiculus) in botany. It is also known as the seed stalk.

Original comment by: dws409

[planteome-user]

The problem with seed funiculus is that it is not part of an organ (since a seed is not an organ), so it can't technically be classified as a cardinal organ part. Perhaps we could redefined cardinal organ part to say that it is part of an organ or develops from part of an organ. Then it would include it would cover seed funiculus.

Original comment by: rlwalls2008

[planteome-user]

Re.: "didn't we agree to use 'organ' for these."

Alternatively, we could define this term similar to CARO, which is similar to our definition of plant organ, but not call it a plant organ and thereby lose all the baggage associated with the term "plant organ". That way, we could classify a seed as a multi-tissue structure.

We would then have to figure out some other way of dealing with the parts of a seed (maybe "cardinal part of a multi-tissue structure" instead of "cardinal part of plant organ"?).

Original comment by: rlwalls2008

[planteome-user]

Can 'organ' be a narrow synonym for this?

Original comment by: jaiswalp

[planteome-user]

A narrow synonym, or it could be a subtype (like it is in CARO).

Original comment by: rlwalls2008

[planteome-user]

I think this might be a solution to the problem we are having, but (I feel) we should keep plant organ as a subclass.

Propose revised def'n: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) 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.

Original comment by: cooperl09

[planteome-user]

• priority: 7 --> 8

Original comment by: cooperl09

[planteome-user]

'fruit distal end/fruit tip/apex' sounds like a 'portion of plant structure'? Similar to the root tip and its regions we have.

LOL: we should keep plant organ as a subclass.

works.

Original comment by: jaiswalp

[planteome-user]

Agreed- and we will need to work on the definition and perhaps the name as well. multi-tissue plant structure sounds like it should be just a collection of tissues.

Original comment by: cooperl09

[planteome-user]

We don't have a term for "portion of plant structure". Perhaps PJ you are referring to cardinal organ part, which is currently (incorrectly) parent to fruit distal end (since fruit is not an organ) and (correctly) parent to root tip. I suggested adding the term "cardinal part of multi-tissue structure" to be more broad than cardinal organ part and encompass things like fruit distal end.

Re. "multi-tissue plant structure sounds like it should be just a collection of tissues.": My original suggestion was that multi-tissue structure should be just a collection of tissues, so that it would be a parent to cardinal organ part. However, I retracted that suggestion in order to be more in keeping with CARO's definition, which says that multi-tissue structure should form "a single distinct structural unit". It is a question of how closely we want to mirror CARO for consistency across ontology versus making new terms that may work better for plants but are less compatible with other anatomy ontologies.

Original comment by: rlwalls2008

[planteome-user]

Based on the discussions at POC conf call 6-12-12, we added this term to test: multi-tissue plant structure (MTPS) (PO:0025496): A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) 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.

is_a plant structure, has sub-classes: PO:0025497: collective plant structure, PO:0009001 fruit ; PO:0009008: plant organ; PO:0009010: seed

Original comment by: cooperl09

[planteome-user]

This term was accepted at the POC meeting on 6-19-12.

Revised definition: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.

(removed the word "distinct" and added "primarily" before bona-fide)

Proposed new comment, based on discussion from the meeting: Most multi-tissue plant structures have at list a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047).

Original comment by: rlwalls2008

[planteome-user]

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

Original comment by: rlwalls2008