Difference between revisions of "POC Conf. Call 1-25-11"
| Line 155: | Line 155: | ||
submitted by Rich Zobel (Nov 2009) | submitted by Rich Zobel (Nov 2009) | ||
| + | |||
| + | |||
| + | |||
| + | |||
Revision as of 18:40, 3 January 2011
POC meeting, Webex Conference Call; Date: Tuesday Jan 25th, 2011 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC Conf. Call 1-11-11?
User requests still open on Source Forge; PSO
Legume terms
submitted by Austin Mast
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
Fascicle The term fascicle can refer to different structures in different taxa. Suggest we use the term Fabaceae fascicle in this case.
Suggested def: A reproductive shoot system that ...
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in that two to several flowers are initiated in each bract axil rather than just one as in a raceme. The cluster of flowers at each node is called a fascicle. The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows the fascicle to be a short shoot topped by a second order inflorescence apical meristem. This meristem initiates flowers in a bilaterally symmetrical order: a single abaxial flower, then two lateral flowers, another median abaxial, then two more laterals. The number of flowers per fascicle depends on the duration of the axillary inflorescence apex of the short shoot, which ceases activity after initiating the few flowers in the fascicle. No flowers are initiated adaxially (toward the first order axis) on the short shoot (Tucker, 1987b; Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be distinguished from a cyme in that every flower is bract subtended in a pseudoraceme." Source: Tucker, 2003, Flora
Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
We added the term stipule spine. Could also add the term stipule bristle: A stipule that is (?)
Alternative is to suggest bristled to PATO
Phyllode Suggested def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
Banner (as in a legume flower) - maybe name Fabaceae banner
Suggested def: A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
Wing (as in a legume flower) - maybe name Fabaceae wing
Suggested def: One of two petals that is adjacent to the banner in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner and keel.
Keel (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name Fabaceae keel
Suggest three new terms:
fused petal: A petal that is fused to another petal. Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
fused corolla: A corolla in which the petals are fused. Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
keel: A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae. Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
Locule The term locule can be used to refer to the cavity in an carpel (an embryo sac and the carpel tissue that surrounds it) or in an anther (a pollen sac and the stamen tissue that surrounds it. In the PGDSO, we have the term PO:0001026 locules established, which is an anther development stage. For clarity, we may want to add two terms: anther locule and carpel locule .
anther locule: A cardinal organ part that is part of an anther and has as parts a single pollen sac and the layers of anther tissue that surround it.
carpel locule: A cardinal organ part that is part of a carpel and has as parts an embryo sac and the layers of anther tissue that surround it and contains at least one ovule. Comment: The embryo sac may have one or more ovules in one locule or may be divided into mutliple locules, each containing an ovule. (needs work)
TraitNet requests
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
child of stem (PO:0009047).
Their comment: is synonym to Tubercle
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
proposed def:
definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
We dealt with this under terms without is_a parents
definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
We could add this term as a kind of upper level bin term (similar to trichome)
Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
from Crum (2001): a cluster of fern sporangia from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
Part_of vascular leaf, has_part sporangium
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
tendrils can derived from multiple types of structures. Suggest we make separate terms:
branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
Can add other types of tendrils if they come up or users need them.
Adding/modifying the root terms
submitted by Rich Zobel (Nov 2009)
Because of the arrangement of develops_from and part_of relations, the annotations for Zea anthers are being carried up to inflorescence branch. This doesn't really make sense. May need to re-examine part_of relations or definition of tassel branch.
User requests still open on Source Forge; PGDSO
tuber growth and development stages
This item has been open on SF since 6/2009
I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
Suggested stages:
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
-tuber initiation
-tuber growth
-tuber maturation
How we work these in will depend on restructuring of PGDSO
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
terms for seed development stages
This is a fairly new request for terms for cotton
