POC Conf. Call 1-4-11

POC meeting, Webex Conference Call; Date: Tuesday Jan 4th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC Conf. Call 12-22-10?

Issues arising from last week's meeting

inflorescence and infructescence branch orders, secondary inflorescence

There was some debate last week about whether or not to name the sub-inflorescences that arise from the main inflorescence axis primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders.

We don't have terms for different vegetative branching orders (outside the inflorescence), but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes.

We do have terms for inflorescence branch orders:

inflorescence axis (PO:0020122): A shoot axis that is part of an inflorescence. [describes any order axis in an inflorescence]

inflorescence branch (PO:0009081): Any branch forming from the primary or the higher order inflorescence axis.

second order inflorescence branch (PO:0006321): Any branch forming from the primary or first order inflorescence branch.

third order inflorescence branch (PO:0006322): Any branch forming from the second order inflorescence branch.

We don't have terms for first order inflorescence branch or primary inflorescence axis, so it is unclear if the use of the phrase "first order branch" in the definition of second order inflorescence branch refers to the main axis or a branch from this axis. This makes all of the definitions ambiguous, but since they have annotation attached to them, we cannot change them until it is clear what they mean.

All of the annotations for second order inflorescence branch are from QTL, and most of them are for genes called "primary branch" or "primary branch length" Most of the annotations for third order inflorescence branch are for a gene called "secondary branch."

• Also need to add terms for infructescence axis and branches.

• Proposed term names and definitions (may change, depending on resolution of inflorescence branch order names):

secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower

secondary infructescence: A reproductive shoot system that is part of an infructescence and has a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit

sensu terms

RW replaced all of the ~80 term names that were structure (sensu Taxon) with Taxon term. However, there were three terms we had changed in November [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] that were obsoleted and replaced with new terms, rather than being renamed. Either we should unobsolete these terms and rename them or obsolete all the terms with sensu in their names. Not clear why they needed to be obsoleted for a renaming.

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

corm

proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.

child of stem (PO:0009047).

podarium

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:

pneumatophore

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.

stele

We dealt with this under terms without is_a parents

diaspore

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)

cone

Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?

sorus

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

tendril

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)

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

Upcoming meetings 2011:

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Laurel, Ramona, DWS and Justin Preece are attending. PJ may attend for the weekend only as he is teaching. Alejandra cannot attend.

PO Activities at PAG:

• Computer Demonstration:

Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)

• Plant Phenotypes workshop and panel discussion:

" The Plant Ontology: Linking phenotypes and genomics across plant taxa"

Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am

• PAG_2011_Collaborators_Workshop and meeting with collaborators

Sunday Late Morning:

Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)

PO Workshop Reg'n site and Survey

• Poster: link to abstract TBA

• Outreach Booth being organized by MaizeGBD- More info TBA

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.

No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.

Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted the organizers to figure out how to nominate additional speakers, and will pass on information to the speakers. We hope to use the 6th time slot for a discussion session.

RW heard from organizers re. additional speakers. Will forward their information. Still waiting to hear about discussion session.