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)
Terms from open SourceForge Trackers
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 (PO:0025066) (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 it a child of 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: (See SF Tracker: leaf rachis)
current def'n: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ)
- peduncle: (peduncle)
current def'n: 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.
proposed def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).
- pedicel: (See SF Tracker: pedicel)
current def'n: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]
proposed 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.
7. More new is_a children of cardinal organ part
(See SF Tracker: new is_a children of cardinal organ part)
*receptacle: (See SF Tracker: receptacle)
Current def'n: The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].
proposed 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(See SF Tracker: hypanthium)
Current def'n: 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.
proposed def'n:
made part_of receptacle instead of part_of flower
- pulvinus: (See SF Tracker: pulvinus)
Current def'n: 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]
-currently is_a (an) organ
proposed def'n:
