Difference between revisions of "POC Conf. Call 2-01-11"
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Revision as of 00:40, 27 January 2011
Goals and Priorities for the next round of revisions:
Publications
-TIPS: An abstract/proposal was submitted to Trends in Plant Science on Dec 31st, 2010. Unfortunately, it was declined. Need to think about another journal that would be appropriate for a short review/update type paper. Possibly add an example of an analysis using PO terms. Possible target journal: 'Current Opinions in Plant Biology'
-Plant Physiology: RW and LC are working on an outline for a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, including restructuring of PSO and PGDSO. Will focus on how PO is now applicable to a wider range of plant species.
- Others? Maybe a short topics paper for American Journal of Botany?
While we were at PAG, DWS mentioned the editor of AJBOT wants him to put together a short paper for them- maybe can focus on PO?
This is also a requirement for OBO Foundry acceptance (see discussion below).
Action items:
Compliance with OBO Foundry guidelines
- All but 3 terms now have is_a parents. The last three will be dealt with when we restructure the PGDSO
- Restructuring of PGDSO should make PO compliant with BFO.
-need to double check that all terms have text definitions
User requests need to be cleaned up and used to fill-in PSO that we have created
- Deal with and complete the list of user requests on SourceForge see: POC_Conf._Call_2-01-11.
- Begin with terms for mosses, requested by Physcomitrella group. If we can get their terms in by the next release, they will use PO instead of creating their own ontology.
TAIR requests on SF: stomatal meristemoid cell ovary septum vs carpel septum dispersed meristematic cell
Restructuring descendants of leaf (PO:0025034)
-many of the part_of children of vascular leaf can also be part of non-vascular leaf. This needs to be done before we can add terms for bryophytes.
Reproductive structures across plants:
- Terms used by model systems (Physcomitrella, Selaginella, Loblolly pine, poplar etc.), and terms are needed for the EST library from the Genomics of Seed Plants project.
- We should establish 'working groups' to add lower level terms? For example: RW and DWS (and MAG?) could work together to add the terms using the NYBG numberspace
Plant Growth and Development Stage Ontology restructuring
A. overall structure:
In the fall LC, RW and BS worked on restructuring PGDSO to meet BFO standards. Have a proposal to show group. For next meeting- 02/01/11??
B. Framework for non-angiosperm terms
As we work on a new overall structure, need to be sure it provides a framework for non-angiosperm terms
New terms for non-angiosperm structures
- Ramona has a long list of new terms to add, but we need to choose an area for focus
Should start with the terms needed by the Physco group, plus terms for reproductive structures (see #4 above)
User requests still open on Source Forge
user requests PSO
Miscellaneous/oldest
procambial cells/dispersed meristematic cells
TAIR requested the term 'dispersed meristematic cell'
This terms is probably best incorporated as a synonym of leaf procambial cell (new term). See SF tracker item for details of discussion.
Suggest using the following hierarchy:
meristematic cell (PO:0004010)
-[is_a] procambial cell (new)
- -[is_a] leaf procambial cell (new); synonym: dispersed meristematic cell
procambium (PO:0006074)
-[is_a] leaf procambium (new)
- -[part_of] leaf procambial cell (new)
Proposed defintions:
procambial cell: A meristematic cell that is part of a portion of procambium. part_of procabium
leaf procambrium: A portion of procambrium tissue that is part of a leaf. part_of leaf
leaf procambial cell: A procambial cell that is part of a leaf procambium. part_of leaf procabium syn: DMC, dispersed meristematic cell
ovary septum vs. carpel septum
There was a request for a new term 'ovary septum.' but after a long discussion on SF, the conclusion seems to be that ovary septum should be a synonym of carpel septum.
Current definition of carpel septum: A thin partition or membrane that divides multilocular ovary. Often found in species with syncarpous (multiple carpels fused) pistil. [source: GR:cwt, GR:pj]
Suggest placing the second sentence in a comment and removing the word often.
Suggested definition: septum that divides a multilocular ovary. Comment: Found in species with syncarpous gynoecia (fused carpels). Synonym: ovary septum
Current definition of septum is: A thin partition or membrane that divides a cavity or a mass of tissue, e.g., in anther, ovary or fruit. [source: APWeb:Glossary], is_a portion of plant tissue.
Suggest that septum should be a cardinal organ part, rather than a portion of plant tissue.
Proposed definition of septum: A cardinal organ part that forms a partition that divides a cavity formed by the fusion several plant structures such as anthers or ovaries.
Comment: A septum is formed by the fusion of the walls of two adjacent organ parts (ovaries or anthers).
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."
Suggested 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 bristles: A stipule that has a brush-like appearance.
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) - suggest using name 'banner petal'
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) - suggest using name 'wing petal'
Suggested 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 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 or in an anther. 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: locule, anther locule and carpel locule.
anther locule: A plant anatomical space that is a cavity in an anther formed by a single pollen sac.
carpel locule: A plant anatomical space that is a cavity in a carpel that contains at least one ovule. Comment: A syncarpous gynoecium may have multiple locules, and the locules of multiple carpels may be fused.
May want to add general parent terms locule: A plant anatomical space that is a cavity within a sporophyll. Synonym: loculus
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)
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
