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tuber and shoot axis tuber #127

Closed planteome-user closed 9 years ago

planteome-user commented 14 years ago

Right now, tuber is_a shoot. Should probably be is_a stem, but this will depend on how we define shoot and stem.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/127

planteome-user commented 14 years ago

At the POC conference call June 23rd, we all agreed that tuber is_a stem

Current definition: Swollen storage shoot with determinate growth.

Proposed definition: An enlarged, short, fleshy underground stem, such as that in the potato. (REE, 4th edition) I would suggest we use: An enlarged, short, fleshy underground stem, and put a comment: such as that in the potato.

Original comment by: cooperl09

planteome-user commented 14 years ago

upgrading to 8 as this impacts several of our other terms

Original comment by: cooperl09

planteome-user commented 14 years ago

proposed def'n: A swollen or enlarged storage stem with determinate growth.
This would encompass both subterranean and aerial tubers.

Original comment by: cooperl09

planteome-user commented 14 years ago

new proposed def'n: A swollen or enlarged storage stem

comment: may have with determinate growth.

Original comment by: cooperl09

planteome-user commented 14 years ago

It have scales leaves subtending axillary buds. I go with shoot. A stem does not necessarily have leaves.

Original comment by: dws409

planteome-user commented 14 years ago

As per discussion at POC meeting on 6/30/10, a tuber is a secondary axis, which equals branch (PO:0025073).

Proposed definition:A swollen or enlarged storage branch with determinate growth. Comment: May bear scale leaves and subtending axillary buds. Found in potatoes.

See comment under granparent term shoot axis that is may bear leaves and branches.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

Accepted definition: A swollen or enlarged storage branch.

We will probably wan to change this definition later, because it is inconsistent with the PATO definition of swollen.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

Suggest removing the word "swollen" from the definition. PATO defines swollen as a temporary enlargement, which this is not. We can just use enlarged.

Proposed definition: An enlarged storage branch.

Original comment by: rlwalls2008

planteome-user commented 14 years ago

That works well.

Original comment by: dws409

planteome-user commented 12 years ago

I made a slight change to the definition and comment of tuber and added a comment.

tuber (PO:0004543), new def.: A radially enlarged storage branch.

comment: This term should be used for tuber derived from branches, as found in potatoes, yams, and other species, not for tubers derived from roots. Use the term tuber root (PO:0025476) for tuber derived from roots, as in Cassava.

Added the same comment to subterranean tuber (PO:0004547).

Original comment by: rlwalls2008

planteome-user commented 12 years ago

Using the phrase "storage branch" (or storage root, for roots), suggests that we have a term called "storage branch".

Maybe it would be better to say "A radially enlarged branch that functions in storage."

We may want to put the last part in the comment.

Original comment by: rlwalls2008

planteome-user commented 11 years ago

Currently: tuber: PO:0004543: A shoot axis (PO:0025029) that is radially enlarged and develops from a branch (PO:0025073), but this cannot be the parent for the tuberous root tubers of species such as Cassava.

Propose new parent term: tuber: (new PO ID): A plant axis (PO:0025004) that is radially enlarged and develops from a branch (PO:0025073) or a root ( PO:0009005).

At the POC conf calll 11-20-12: ''DWS: Suggest to leave off the last phrase: and just define it as: tuber: (new PO ID):''' A plant axis (PO:0025004) that is radially enlarged'', but I think it will be helpful to have that extra information- we could put it in the comment.

I propose we rename the existing tuber term and make it a sub-class of the new tuber term:

shoot axis tuber (PO:0004543): A tuber that is a radially enlarged shoot axis (PO:0025029) and develops from a branch (PO:0025073).

Existing Comment: Functions in storage of photosynthate metabolites. This term should be used for tubers derived from branches, as found in Solanum spp. (e.g. potato) or Dioscorea spp. (e.g. yam) and other species.

Revised: Use the term tuberous root tuber (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis.

Original comment by: cooperl09

planteome-user commented 11 years ago

Propose revised definition: shoot axis tuber (PO:0004543): A tuber (PO:0025522) that develops from a branch (PO:0025073).

We do not need to repeat that it is a radially enlarged shoot axis (PO:0025029), since that is part of the parent definition.

Original comment by: cooperl09

planteome-user commented 11 years ago

new term: tuber: (PO:0025522): A plant axis (PO:0025004) that is radially enlarged.

Comment: Functions in storage of photosynthate metabolites. May develop from a branch (PO:0025073) or a root (PO:0009005). If you are annotating to tuber, you should pick the more specific child term: shoot axis tuber (PO:0004543) and tuberous root tuber (PO:0025476).

Original comment by: cooperl09

planteome-user commented 11 years ago

.........shoot axis tuber (PO:0004543) and tuberous root tuber (PO:0025476).

Think this should be 'or' not "and"

Original comment by: dws409

planteome-user commented 11 years ago

Revised comment: Functions in storage of photosynthate metabolites. May develop from a branch (PO:0025073) or a root (PO:0009005). If you are annotating to tuber, you should pick the more specific child term: shoot axis tuber (PO:0004543) 'or' tuberous root tuber (PO:0025476).

thanks !

Original comment by: cooperl09

planteome-user commented 11 years ago

shoot axis tuber (PO:0004543): A tuber (PO:0025522) that develops from a branch (PO:0025073).

If this type of tuber always develops from a branch, perhaps this should be named a "branch tuber"?

Original comment by: cooperl09

planteome-user commented 11 years ago

Currently diaspore is a broad synonym of shoot axis tuber, as well as bulb, corm, fruit, plant spore, and seed.

The only def'n I can find for diaspore is:

In botany, a diaspore is a plant dispersal unit consisting of a seed or spore plus any additional tissues that assist dispersal. (wikipedia)

So I am not sure if this is appropriate.

Original comment by: cooperl09

cooperl09 commented 8 years ago

Revised hierarchy for tubers: Was: shoot axis tuber (PO:0004543): A tuber (PO:0025522) that develops from a branch (PO:0025073). Revised: shoot axis tuber (PO:0004543): A shoot axis (PO:0025029) that develops from a branch (PO:0025073) and is radially enlarged for storage.