POC Conf. Call 12-28-10

POC meeting, Webex Conference Call; Date: Tuesday Dec 28th, 2010 10am (PST)

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU).

Absent: Justin Elser (OSU), Alejandra Gandolfo; (Cornell University), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Acceptance of the minutes from the POC Conf. Call 12-22-10?

There were no additions, deletions or changes to the minutes of the last meeting.

Musa requests still needing to be resolved:

Issues arising from new terms:

• petiole canal: The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole

Added term 'adaxial petiole': A cardinal organ part that is the adaxial portion of petiole. Comment: Adaxial petiole may be concave or form a canal. Narrow synonym: petiole canal.

Also added abaxial petiole, with parallel definition.

Now that we have plant anatomical space, maybe we should add petiole canal as a space? See tracker for canal

All present last week agreed that canal should be a plant anatomical space, BS suggested we check FMA. They do not have canal per se, but classify canals as organ cavities (e.g., lumen of anal canal is part_of lumen of intestine, which is an organ cavity subdivision).

Proposed definition of canal: A plant anatomical space that is roughly linear or cylindrical in shape. Comment: May be enclosed within a plant structure or on the surface of a plant structure.

new proposed def'n of petiole canal: A canal that is part of a petiole. Comment: May occur on the surface or be internal.

Can make children abaxial petiole canal and adaxial petiole canal: a petiole canal on the ab/adaxial surface of a petiole.

Canal: Revised proposed def'n: A plant anatomical space that iseither a groove on the surface or a tube in the interior. Comment: May be cylindrical (ref: PATO?) in shape, enclosed or on the surface of a plant structure.

BS: need to address connectivity of plant parts, see Virtual Physiological Human (VPH) site

• Fused tepal: Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642).

This will cover the individual tepals that are fused, but they have requested the term Compound tepal: The outer perianth sheath of 5 fused tepals which has 3 major lobes and 2 minor ones.

Suggest we add new term fused collective tepal structure: A collective tepal structure which has as parts at least two fused tepals. Exact synonym: compound tepal, subset for Musa

accepted

Musa flower terms

• crown: The raised ridge of tissue to which the pedicels are attached.

Is this part of an inflorescence, part of an inflorescence axis?

This refers to the inflorescence axes between individual flowers that do not elongate. It is a shoot system that is part of the inflorescence (which is also a shoot system).

Added the following term:

• Musa crown (PO:0025134): A shoot system that forms the basal part of an inflorescence in Musa species to which the pedicels are attached and in which the internodes do not elongate, giving the appearance of a ridge of raised tissue.

is_a shoot system, part_of inflorescence

• basal flower: First flowers emerging on the inflorescence with the potential to give rise to fruits. part_of CO_125.0000136 ! basal bud

Do we want to describe different flowers on the infloresence? If so, we could add general term basal flower: a flower at the proximal end of on an inflorescence. Comment: in Musa, the basal flowers are the first to emerge and have the potential to give rise to fruits.

• male bud: The usually persistent bud when it is only composed of bracts with male flowers. is_a: CO_125.0000146 ! bud; is_a: CO_125.0000146 ! bud

Proposed definition: An inflorescence bud that develops into a male inflorescence.

If we go this route, we will need to add male, female and hermaphrodite reproductive bud, male, female and hermaphrodite inflorescence bud, male, female and hermaphrodite floral bud, and male, female and hermaphrodite inflorescence, plus the floral terms described above.

At the 11-5-10 POC meeting, we decided not to add separate terms for male and female flowers. Probably want to be consistent with bud.

Inflorescence and infructescence

The Musa fruit terms deal with infructescence parts. Before we define them, we need a solid definition of inflorescence and infructescence that follow the genus/differentia form.

Current definition of inflorescence: That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers, is_a reproductive shoot system.

Proposed definition of inflorescence: a reproductive shoot system that has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and all of the flowers borne by those axes. Must have two or more flowers as parts.

Current definition of infructescence: The grouping or arrangement in which fruits are borne on a plant.

Proposed definition of infructescence: a reproductive shoot system that develops_from an inflorescence and has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and all of the fruits borne by those axes.

Musa fruit terms

• bunch: The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD

This could be a narrow synonym of infructescence (PO:0006342). Not sure what they mean by rachis in this definition - probably the main axis of the infructescence.

• hand of fruits: All the fruits that develop in the axil of a single bract. part_of CO_125.0000014 ! bunch

A Musa inflorescence is a compound spike. A branch of the spike develops from the axil of a single bract. This branch branches again to form a subdivision of the spike (spikelet), which when mature produces a 'hand' of fruits. All of the subdivisions of the compound spike together, when mature, are a bunch of bananas. A hand is a subdivision of an infructescence that develops from a subdivision (spikelet) of an inflorescence (compound spike).

We already have the term inflorescence branch (PO:0009081), is_a branch, but this refers specifically to a shoot axis, not the entire branching part of an inflorescence. Suggest we add term infructescence branch (is_a branch, develops from inflorescence branch). We need terms to refer to the subdivisions (loosely called branches, but not branches in as PO defines them) of an inflorescence or infructescence.

Suggest two new terms:

inflorescence subdivision (maybe we can come up with a better name): A reproductive shoot system that is part of an inflorescence and has a parts an inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence

spikelet (PO:0009051) would be a child of this term.

infructescence subdivision: A reproductive shoot system that is part of an infructescence and has a parts an infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence

• flower relics: Remains of a female flower when it persists on the fruit. part_of CO_125.0000033 ! fruit

Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.)

Musa shoot terms

• sucker: Lateral shoot that develops from the corm and usually emerges close to the parent plant. is_a: CO_125.0000001 ! plant part

This could be a synonym of axillary shoot system (PO:0006343): A shoot-borne shoot system that develops from an axillary vegetative bud.

Will probably need to be a broad synonym, because (I think) people also use the term sucker to refer to root-borne shoots. Alternatively, we could make the phrase "Musa sucker" a narrow synonym of axillary shoot system, and make "sucker" a synonym of root-borne shoot.

• pseudostem: 'False stem' of cylinders formed by the concentric leaf sheaths through which the peduncle later grows. is_a: CO_125.0000001 ! plant part

Could this be a collective phyllome structure (it is only composed of petioles, not phyllomes)? If not, we could make it a collective plant structure. If this structure is unique to Musa, we should call it "Musa pseudostem," but maybe it occurs in other taxa?

• pseudostem underlayers: Abaxial side of the inner sheath which is not visible until the outermost sheath has been removed. part_of CO_125.0000046 ! pseudostem

This is the abaxial portion of a leaf sheath (PO:0020104). We could make a new term leaf sheath abaxial epidermis (sibling of petiole abaxial epidermis, is_a leaf epidermis), and add pseudostem underlayer as a narrow synonym.