POC Conf. Call 6-30-10

POC meeting, Webex Conference Call; Date: June 30th, 2010 10am (PDT)

In attendance: POC members:

Collaborators:

Absent:

Acceptance of the minutes from the 6-29-10 meeting? All in favor?

Workshop page: [Corvallis Workshop June 29th and 30th, 2010]

*Work on items from Tuesday morning:

-Ontology development - Include local botany experts?

• Open SF tracker items -- changes that have been made but not approved by group.

-Still need to resolve stem and shoot (affect tuber terms, since tuber is_a shoot, but, e.g., tuber cortex is_a stem cortex)

1. stem (PO:0009047) stem

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

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

Synonyms: cane, culm, stalk, trunk

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

2. Shoot (PO:0009006) (need to add SF item for shoot)

current def'n: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems. [source: POC:curators]

Problem: Shoot has no is_a parent- should be a collective plant structure or a plant organ?

3. Tuber (PO:0004543) (need to add link to SF tracker)

current def'n: Swollen storage shoot with determinate growth. [source: POC:curators] proposed def'n: A swollen stem with determinate growth that has part portion of storage parenchyma.'

We should request the term determinate from PATO. Tuber is already defined as determinate growth.

'Subterranean tuber' is_a 'tuber' and part_of 'rhizome', so its definition should be: 'A tuber that is part of a rhizome.'

subterranean tuber is 'A swollen rhizome or a part of the rhizome with determinate growth. [source: POC:curator]' and

'aerial tuber'-?

4. rhizome (PO:0004542) (need to add link to SF tracker)

rhizome is 'Underground shoot. [source: POC:curators]'

5. Stolon (PO:0003024) (need to add link to SF tracker)

current def'n: A slender, prostrate or trailing above-ground stem which produces roots and sometimes erect shoots at its nodes. [source: APWeb:Glossary]' but it is classified as a shoot.

6. 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.

current 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)

*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