New term for root tuber

[planteome-user]

Need to define two terms clearly under 'plant structure' for 'tubers'

http://www.plantontology.org/amigo/go.cgi?xpand=[PO:0004543](http://purl.obolibrary.org/obo/PO_0004543)&search\_constraint=terms&query=[PO:0004543](http://purl.obolibrary.org/obo/PO_0004543)&view=details&show\_associations=list they should be root tuber and stem/shoot tuber. The current term PO:0004543 : tuber is suggesting only a shoot/stem tuber only.

Pankaj

Reported by: cwtung

Original Ticket: obo/plant-ontology-po-term-requests/47

[planteome-user]

We currently have the terms aerial tuber and subterranean tuber which should take care of this. The term root tuber is not technically correct (since tubers are shoots), and should be avoided.

Original comment by: rlwalls2008

[planteome-user]

We have terms subterranean tube and aerial tuber to deal with this request. I am closing this item, since it has been on the POC meeting agenda for several weeks.

Original comment by: rlwalls2008

[planteome-user]

I am reopening this item.

Dennis and I were reviewing different types of tubers, and realized that we should have a new term for root tuber. This would be is_a root and would be separate from the existing term tuber (PO:0004543). PO:0004543 should probably be renamed shoot tuber, but its definition is okay. Can add comment that shoot tubers can be distinguished by scale-like leaves and/or axillary buds. Root tubers can often be distinguished by have lateral roots or their remnants. Sometime root tubers have vegetative buds on them like shoot tubers, but these arise from adventitious buds.

Original comment by: rlwalls2008

[planteome-user]

I agree that it is a good idea to create a new term to describe the storage root tubers in plants like Cassava, but I think naming it root tuber will be confusing as we have the shoot axis aerial and subterranean tubers already.

I suggest the following:

storage root (PO:xxxxxxx): A root (PO:0009005) that is enlarged and specialized for storage. (or something to that effect)

This would also make it (more or less) consistent with the Cassava ontology at GCP (http://www.cropontology.org/ontology/CO\_334/Cassava)

Comment by RW is ok, except for minor change suggested (in italics) :

Comment: A ''storage root'' may be distinguished from a ''shoot axis'' tuber (PO:0004543) by the presence of a root cap (PO:0020123) when very young, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes a ''storage root'' bears vegetative buds (PO:0000058) like a tuber of the shoot axis (PO:0025029), but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the shoot-borne root is attached. A ''storage root'' often develops from a shoot-borne root (PO:0000042).

We could add 'root tuber' as a synonym

This will prevent having to rename the 48 subtypes of tuber (PO:0004543), as suggested 'shoot tuber' (should probably be shoot axis for clarity.. Many of the these already have very long names For example: subterranean tuber axillary vegetative bud (PO:0025042) would become: subterranean shoot (axis) tuber axillary vegetative bud.

Original comment by: cooperl09

[planteome-user]

We had a discussion of this at the POC meeting on 4-24-12. We agreed that it would be problematic to change the names of all of the existing terms, but were concerned about using the name "storage root" because just about any type of root can be involved in storage.

There is a legitimate concern that when people search for tuber for, e.g., a potato, and see "root tuber", they may be tempted to use that instead of "subterranean tuber", which is the correct term. However, "root tuber" is the name that most people use for this structure.

I will add a term to the developers' file and call it "tuber root". This might make it clearer that it is a root. We can add comments to both kinds of tubers, in hopes that people will actually look at the definition.

We also agreed that the definition of both tuber and tuber root should say "radially enlarged" instead of just "enlarged".

Original comment by: rlwalls2008

[planteome-user]

Added new term.

tuber root (PO:0025476), proposed def.: A radially enlarged root (PO:0009005).

comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuber root may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuber roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuber root is attached. A tuber root usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).

Original comment by: rlwalls2008

[planteome-user]

Based on further discussions- we created a new term: tuberous root (PO:0025523): A root (PO:0009005) that is radially enlarged relative to other lateral roots (PO:0020121) or shoot-borne roots (PO:0000042) on the same plant, but not as enlarged as a tuberous root tuber (PO:0025476).

Renamed the exisitng term: tuberous root tuber: (PO:0025476): A tuber (PO:0004543) that develops from a tuberous root (PO:0025523) and is further radially enlarged.

add relationship: tuberous root tuber develops_from tuberous root.

Original comment by: cooperl09

[cooperl09]

Revised hierarchy for tubers to ensure a path to the anatomical structure : Was: tuberous root tuber (PO:0025476): A tuber (PO:0004543) that develops from a tuberous root (PO:0025523) and is further radially enlarged.

Revised: tuberous root tuber (PO:0025476): A root (PO:0009005) that develops from a tuberous root (PO:0025523) and is further radially enlarged for storage.

• Maintained the other is_a parent link to tuber for now.

See also Issue #127

[DarioJCavaliere]

Propose renaming: tuberous root tuber (PO:0025476) to root axis tuber

Currently, shoot axis tuber (PO:0004543) and tuberous root tuber (PO:0025476) are subclasses of tuber (PO:0025522). We propose renaming tuberous root tuber (PO:0025476) to root axis tuber, in an effort to keep the subclasses parallel.

[cooperl09]

While I agree that this change might appear to be better, there are a couple of important considerations.

• The tuberous root tubers arise from special types of roots (tuberous roots), which are either lateral roots or shoot-borne roots, which was why we created the term "tuberous root (PO:0025523).
• The name 'tuberous root' is widely used in the literature; for example: https://scholar.google.com/scholar?q=Tuberous+roots&btnG=&hl=en&as_sdt=0%2C38
• root axis is not a PO term, thus it will be confusing to users. So we will change it to say a root axis tuber develops from a tuberous root? That name not clear because it sounds like it can arise from any kind of root.
• Currently the tuberous root tuber (PO:0025476) already has the exact synonyms 'root tuber' and also 'storage root', so it is easily found by anyone looking for that this structure.
• We could swap the root tuber synonym and the term name, but I don't think that actually makes that big of a difference, and does not accomplish what you are trying to do. Not all sibling classes need to be directly parallel to each other.