POC Conf. Call 7-05-11
POC meeting, Webex Conference Call; Date: Tuesday June 14th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_6-28-11?
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 floral fascicle or flower fascicle in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
From Tucker, 2003, Flora: (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."
Proposed def: A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated. Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
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 has a brush-like appearance.
Alternative is to suggest bristled to PATO
Proposed 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) - suggest using name 'banner petal'
Proposed 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) - suggest using name 'wing petal'
Proposed def: One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla 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 'corolla 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.
corolla keel: A fused corolla that consists of the two lowest petals of a corolla.
Comment: Found in some flowers of the Fabaceae. 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.
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.
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 and lacks a lamina. Comment: Aids plant in climbing.
leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.
Can add other types of tendrils if they come up or users need them.
Alternative is to create a parent 'tendril'(is_a plant structure) with children that are part_of the other structures:
tendril
is_a leaf tendril part_of leaf
is_a stem tendril part_of stem
is_a branch tendril part_of branch
root terms
Submitted by Rich Zobel (Nov 2009).
Still need to work on definitions for these terms.
User requests still open on Source Forge; PGDSO
terms for seed trichome development stages
Open since 07-28-2010
Request
The following terms have been requested for cotton fiber development (their structure and defintions):
seed development stages PO: 0001170
---[part_of]Seed hair development stages
---[part_of]seed hair initiation stage: The earliest histological evidence of seed hair initiation, ie, a change in the orientation of cell division in the ovule epidermises occurs at or just before anthesis. (Ruan YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].
---[part_of]seed hair elongation stage: A period of rapid elongation of hair initials without cell division for 16-25 days. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources:PMID: 17905721, PMID: 12671090].
---[part_of] seed hair secondary wall biosynthesis stage: A phase of the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].
---[part_of]seed hair maturation stage: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA). (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].
Suggested terms and definitions:
Do we want to use stage or phase throughout PGDSO?
seed development stages (PO:0001170)
Current definition: Stages of seed development, from fertilization to the dry or quiescent state. [source: TAIR:ki]
Proposed name and definition: seed development stage: A plant structure development stage that begins with fertilization and ends with seed maturation.
Comment: Only used for seed plants. Some seeds may enter a period of dormancy after seed development is complete.
is_a plant structure development stage; part_of sporophyte phase; subset for gymnosperms and angiosperms; add relation: seed participates_in seed development stage
New terms and proposed definitions:
seed trichome development stage: A plant structure development stage that is part of a seed development stage during which one or more seed trichomes develop.
is_a plant structure development stage; part_of seed development stage; add seed trichome participates_in seed trichome development stage
synonym: seed hair development stage
seed trichome initiation stage: The earliest histological
evidence of seed hair initiation, ie, a change in the orientation of cell
division in the ovule epidermises occurs at or just before anthesis. (Ruan
YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].
synonym: seed hair initiation stage
seed trichome elongation stage: A period of rapid elongation
of hair initials without cell division for 16-25 days. (Lee JJ, 2007,
Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964)
[Sources:PMID: 17905721, PMID: 12671090].
synonym: seed hair elongation stage
seed trichome secondary wall biosynthesis stage: A phase of
the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ,
2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell
15:952-964) [Sources: PMID:17905721, PMID:12671090].
synonym: seed hair secondary wall biosynthesis stage
seed trichome maturation stage: A period of seed hair
maturation from 50 to 60 days post-anthesis (DPA).
(Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant
Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].
synonym: seed hair maturation stage
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
Upcoming meetings 2011:
Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.
Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).
Anybody going??
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
Full-Day Workshops Schedule:
July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability
July 26 6.30pm-9pm Evening Workshop: Common Logic
July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium
- LC will attend and represent the PO. Invite other plant people?
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.
Gramene will be putting together a workshop again, focusing on pathways. LC and PJ will present a PO poster.
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
