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 is either a groove on the surface or a tube in the interior of a plant structure. Comment: May be cylindrical (ref: PATO?) in shape, with a circular, D-shaped or other irregularly-shaped cross-section.

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. Also add syntepalous perianth as exact synonym.

PJ: add reference to CO where they are being referred to, LC will check with Rosemary/Elizabeth about the changes that were discussed @ CO- using PO terms rather than CO?

see GCP_Crop_Ontology

GCP used numbers like: CO_125.0000012, but CO is already in use for Cell Ontology, and this has too many digits in the numerical portion, will add xrefs to GCP terms as: CO_125:0000012.

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

Revised term name and def'n: inflorescence branch crown (PO:0025134): A shoot system that forms the basal part of an inflorescence to which the pedicels are attached and in which the internodes do not elongate, giving the appearance of a ridge of raised tissue.

• 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 inflorescence? 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.

This generated a lot of discussion and suggestions of examples; for now 'basal flower' will be added as a synonym of flower, not part of basal bud but develops from basal bud. Need to bring in PATO to help describe the phenotypes and positioning.

RW and DWS will plan a time to work on the descriptions of various types of inforescences.

• 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.

This will go in as a synonym of inflorescence 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.

accepted

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.

synonym of infructescence, subset Musa

• 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

A Musa inflorescence is a raceme of cymes (not compound spike)

There was some debate about whether or not to name the sub-inflorescences that arise from the first order branches primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders. We don't actually have terms for different branching orders yet, but the stem is defined as the primary (not zero order) axis of the plant, which makes the first branches secondary axes. Therefore I (RW) am creating new terms for secondary inflorescence and infructescence. Can add higher orders later if needed.

revised term names and proposed def'ns:

secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a first-order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower

secondary infructescence: A reproductive shoot system that is part of an infructescence and has a first-order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit

• 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.)

revised term names and proposed def'ns: persistent sepal, petal or tepal: ... Common in persimmons, eggplant, tomatoes, peppers, tomatillos, etc

sepal is part of the flower, add comment that it may persist in fruit

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.

Note: 'sucker shoot' is a synonym of PO:0004544 : root-borne shoot system,

need both root-borne and shoot-borne suckers.

• 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.

add notes here...

Note: need to check with Rosemary/Elizabeth whether we should use 'banana' or 'Musa'? Musa is the Genus name.

Other Items:

'sensu' terms

from 12-22-10:

• There are a bunch of terms where the name has been changed from something (sensu Poaceae) to Poaceae something. This means we have a mix of sensu and non-sensu terms.

Should we go through and fix these for this release?

All present were in favor of this, BS: these have been removed by the GO, PO should do the same.

Accepted, approved by PJ, who was not on the call on 12-22

Also, check that we have subset: Poaceae "Term used for grasses", we do

PO Next release

Timeline and Plan for Upcoming Release - complete changes discussed this week, put on Beta browser after Justin E returns from vacation (tomorrow?)

The next set of items should be slated for the nest round of revisions, so we can deal with the annotations, documentation, TIPs paper and preparing for PAG. and also we need to do an 'internal' review before releasing it early in the New Year.

- look for annotations that need to be moved:

- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)

see also Jan 2011_Release_Page

RW will focus on doing the changes to the PSO that have been discussed in the last 2 weeks. Will be done by Thursday, Dec 30th?

TIPS proposal

A abstract/proposal has been circulated.

LC will focus on doing the summarizing the suggested changes to the proposal, needs to incorporate some detail on what is new in the PO, and novel. Also should add additional, more current refs. Will aim for Thursday, Dec 30th or Friday for submission

PJ: suggested a collaboration with Nick Provart of BAR on the analysis, but I am not sure if this was for the larger paper in 2011...

Dennis will send out something to the group...