POC Conf. Call 2-22-11
POC meeting, Webex Conference Call; Date: Tuesday Feb 22th, 2011 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_2-15-11?
Wrapping up the Physcomitrella terms:
See Terms requested by Physco group for a list of terms.
Completing items worked on last week:
Continuing User requests: for PSO
- Deal with and complete the list of user requests on SourceForge-
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
Upcoming meetings 2011:
- Phenotype Ontology RCN Summit
February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,
Laurel and Pankaj will be attending.
From RW: -What is official PO strategy for dealing with phenotypes?
-Should it differ between description of mutant phenotypes and descriptions needed for systematic studies?
-Should PO develop a list of terms to be submitted to PATO (rather than our current piecemeal suggestions)?
-Possible case study: description of inflorescence types.
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: The deadline for workshop and tutorial proposals for the ICBO conference has been extended to February 15th, 2011
- We decided we are too shorthanded to put together a PO workshop, but Melissa, Alan and Chris are organizing an anatomy ontology workshop.
- LC will attend and represent the PO. Invite other plant people?
-BS suggested we might want to submit a short paper which could be published in longer form later- see above
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
