POC Conf. Call 4-27-10

POC meeting, Webex Conference Call; Date: April 27th, 2010 10am (PDT)

Agenda:

Acceptance of the minutes from last weeks meeting? All in favor?

Items carried over from last week's agenda:

1. Collective phyllome structure and its children

A. collective phyllome structure (See SF tracker: collective phyllome structure).

Proposed def.:A collective plant structure that consists of two or more phyllomes originating on the stem from the same node or from two or more adjacent nodes with compressed internodes.

Unlike the definition we came up with last week, this definitions does not contain the undefined terms rosette and whorl. It also uses the term stem instead of axis, because stem is defined in the PO, and axis is not.

'Collective phyllome structure' would replace the term original term phyllome whorl (PO:0008033) which we have been calling 'whorled phyllome structure.' The proposed new term phyllome aggregation would be rejected.

'Whorl' and 'floral whorl' (a term used in GO) would be narrow synonyms.

Children (see items B and C below) are androecium, calyx, corolla, epicalyx, gynoecium, collective leaf structure, perianth, rosette, and collective tepal structure (new term proposed by Laurel and Pankaj after the meeting).

Note: Whorls that have been reduced to a single organ will be placed under 'plant organ'.

B. Children of collective phyllome structure: See SF tracker item defintions for children of collective phyllome structure and item C below.

>>Androecium: A collective phyllome structure composed of two or more stamens.

>>Calyx: A collective phyllome structure composed of two or more sepals.

>>Corolla: A collective phyllome structure composed of two or more petals.

>>Epicalyx: A collective phyllome structure composed of two or more phyllomes immediately outside the calyx.

>>Gynoecium: A collective phyllome structure composed of two or more carpels.

>>Collective leaf structure: A collective phyllome structure composed of two or more leaves. Rosette and leaf whorl are synonyms.

>>Perianth: A collective phyllome structure composed of two or more petals, sepals, or tepals.

>>Collective tepal aggregation: A perianth composed of two or more tepals (Child of perianth, see item C below).

The proposed children rosette and whorl would be rejected. Rosette and leaf whorl would be synonyms of 'collective leaf structure' and whorl would be a synonym of 'collective phyllome structure'.

C. New term: collective tepal structure: (See SF Tracker collective tepal structure)

proposed new def'n: A perianth composed of two or more tepals.

is_a perianth

D. tepal (See SF Tracker: tepal)

proposed revised def'n: A phyllome that is part of a perianth in which all parts are similar in appearance and are neither petals nor sepals.

Check out the link to images for tepals on the dev browser: tepal

What do folks think of this as a way to include images in the PO? Is there a way to include images in the obo file?

2. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.

proposed definition (modified slightly from Gleason and Cronquist 2nd edition, via Dennis): A collective plant structure that contains a ripened ovary, together with any other structures that ripen with it and form a unit with it.

Does everyone agree that a fruit is a collective plant structure?

proposed change: fruit is_a 'collective plant structure' and part_of infructescence. (CPS: a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue).

3. Embryo (See SF Tracker: embryo) Def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

-has no is_a parent, propose making it is_a whole plant?

-embryo contained_in archegonium could work for all land plants (maybe not charophytes), rather than contained_in seed (doi: 10.1111/j.1469-8137.2009.03054.x)

Older items

4. stem (See SF Tracker stem)

Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]

Synonyms: cane, culm, stalk, trunk

Problem: Stem has no is_a parent- should be a collective plant structure?

OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.

2. stalk (See SF Tracker: stalk)

This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.

def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.

Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.

-made a cardinal organ part (as per its definition) rather than an organ.

Proposed children of stalk: (Test: do all of these fit the definition?)

• filament: The stalk of a stamen.(stamen:organ)

• petiole: The stalk of a leaf. (leaf:organ)

• petiolule: The stalk of a leaflet (leaflet:cardinal organ part)

• funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)

• gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)

• leaf rachis: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ) (See SF Tracker: leaf rachis)

• peduncle: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves. (See SF Tracker: peduncle)

propose revised def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).

• pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

(See SF Tracker: pedicel)

propose revised def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).

Note: We also have the term 'stem'. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.

3. More 'new is_a children of cardinal organ part' (See SF Tracker: new is_a children of cardinal organ part)

Several weeks ago, we created new children of cardinal organ part, from terms that had no is_a parent. We can deal with definitions and relationships of each term later, but for now we simply need to approve moving them to cardinal organ part.

Some of them can be dealt with later, but the terms listed here are a higher priority and/or can be dealt with very quickly. Many of the definitions need to be worked on at a future meeting. See Source Forge items for additional comments.

*receptacle: The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators]. (See SF Tracker: receptacle)

propose revised def'n: The region at the top of either the peduncle or pedicel where the floral appendages (for example, sepals, petals, stamens, and pistils) are attached.(Brooklyn Botanic Garden http://www.bbg.org/gar2/topics/botany/parts_flowers.html)

Comments: If both pedicel and peduncle is_a stalk, and stalk is_a 'cardinal organ part', then both pedicel and peduncle must be part of some organ for this to work.

*hypanthium- A cup- or tube-like structure bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary of a flower. (See SF Tracker: hypanthium)

made part_of receptacle instead of part_of flower

*pulvinus:-A more or less abrupt swelling, especially at the apex or base of a petiole or leaf sheath, often glandular and/or being the place where a plant responds to touch, gravity or light, in panicoid grasses a swollen region in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary] (See SF Tracker: pulvinus)

-currently is_a (an) organ