Difference between revisions of "POC Conf. Call 5-4-10"

From Plant Ontology Wiki
Jump to navigationJump to search
Line 13: Line 13:
  
  
 +
1. '''Wrapping up the phyllome structures that include 'whorls' and 'rosettes':'''
  
 +
'''collective phyllome structure''' (See SF tracker: [http://sourceforge.net/tracker/?func=detail&aid=2980171&group_id=76834&atid=835555/ collective phyllome structure]).
  
 +
New proposed def'n.:A collective plant structure that consists of two or more phyllomes originating from the same node or from two or more adjacent nodes with compressed internodes.
  
  
−
'''Older items'''
+
This def'n avoids the use of the term 'stem' here. 'Whorl' and 'floral whorl' (a term used in GO) are narrow synonyms.
  
−
'''1. stem''' (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2982923&group_id=76834&atid=835555/ stem])
+
 
 +
'''Items carried over from last week's agenda:'''
 +
 
 +
'''2. fruit''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972169&group_id=76834&atid=835555/ fruit])
 +
 
 +
Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.
 +
 
 +
Proposed def'n: A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it.
 +
 
 +
PJ (via SourceForge) offered a proposed def'n using 'post-fertilization'.
 +
 
 +
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: [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555/ 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 (not charophytes), rather than contained_in seed (doi: 10.1111/j.1469-8137.2009.03054.x)
 +
 
 +
 
 +
'''New (older) items for discussion:'''
 +
 
 +
'''3. stem''' (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2982923&group_id=76834&atid=835555/ stem])
 +
 
 +
Problem: Stem has no is_a parent- should be a collective plant structure?
  
 
Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]
 
Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]
  
 
Synonyms: cane, culm,  stalk, trunk
 
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.
 
OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.
  
  
−
'''2. stalk''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972224&group_id=76834&atid=835555/ stalk])
+
'''4. stalk''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972224&group_id=76834&atid=835555/ 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.
 
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.
Line 64: Line 94:
  
 
'''Note: We also have the term 'stem''''.  We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.
 
'''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: [https://sourceforge.net/tracker/?func=detail&aid=2971884&group_id=76834&atid=835555/ 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: [https://sourceforge.net/tracker/?func=detail&aid=2975273&group_id=76834&atid=835555/ 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: [https://sourceforge.net/tracker/?func=detail&aid=2972200&group_id=76834&atid=835555/ 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: [https://sourceforge.net/tracker/?func=detail&aid=2972236&group_id=76834&atid=835555/ pulvinus])
 
−
 
−
-currently is_a (an) organ
 

Revision as of 17:24, 28 April 2010

POC Conf. Call 5-4-10


POC meeting, Webex Conference Call; Date: May 4th, 2010 10am (PDT)

Agenda:

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


Items carried over from last week's agenda:


1. Wrapping up the phyllome structures that include 'whorls' and 'rosettes': 

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

New proposed def'n.:A collective plant structure that consists of two or more phyllomes originating from the same node or from two or more adjacent nodes with compressed internodes.


This def'n avoids the use of the term 'stem' here. 'Whorl' and 'floral whorl' (a term used in GO) are narrow synonyms.


Items carried over from last week's agenda:

2. fruit (See SF Tracker: fruit)

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

Proposed def'n: A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it.

PJ (via SourceForge) offered a proposed def'n using 'post-fertilization'.

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 (not charophytes), rather than contained_in seed (doi: 10.1111/j.1469-8137.2009.03054.x)


New (older) items for discussion:

3. stem (See SF Tracker stem)

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

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.


4. 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.

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_5-4-10&oldid=842"