POC Conf. Call 2-15-11

POC meeting, Webex Conference Call; Date: Tuesday Feb 15th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_2-08-11?

Restructuring descendants of leaf (PO:0025034)

-Some 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.

-Need to double check the is_a children of leaf.

current is_a children of leaf

• non-vascular leaf - ok as is

• vascular leaf - ok as is

• prophyll (PO:0009042) is_a phyllome and scale leaf (PO:0006003) is_a phyllome (see prophyll and scale leaf).

Suggest making prophyll a child of vascular leaf.

Suggest making scale leaf is_a leaf (because the term could be used to refer to non-vascular leaves, even though it is usually used for vascular leaves.

• Suggest adding frond and needle as exact synonyms of vascular leaf

current part_of children of leaf

• leaf apex - ok as is - applies to both vascular and non-vascular leaf

• leaf base - ok as is - applies to both vascular and non-vascular leaf

• leaf epidermis - ok as is - The term may be used for non-vascular leaves, even though many are only one cell thick.

Need to consider if the definition of epidermis works bryophytes (see section below on Physco terms).

• leaf endodermis -- Is there ever an endodermis in non-vascular leaves? If not, this should be part_of vascular leaf.

current is_a children of vascular leaf

Is there heteroblasty in non-vascular leaves? do these terms apply?

• juvenile leaf

• transition leaf

• adult leaf

Physco group has included these terms in their ontology, but said they are not sure if they are necessary. Said there are differences among phyllids based on their position on the stem (more basal versus more terminal), but the terms juvenile and adult are not necessarily used to describe them. If we want to use them for non-vascular leaves, we either need to make them children of leaf instead of vascular leaf, or add separate terms for vascular and non-vascular juvenile, transition and adult leaves.

Do we want to keep these (as phenotype terms)? At one point we discussed getting rid of them.

• simple leaf

• compound leaf

Terms that are probably okay:

• cotyledon - ok

• leaf spine - ok

• cigar leaf - ok

• rosette leaf - probably ok as child of vascular leaf - Are there ever rosette's in gametophytes?

• cauline leaf - definition is a bit weird, actually applies to leaves that are part of an inflorescence (which we call bracts)

Current def: Leaf or pairs/whorls of leaves borne on the stem. [source: TAIR:ki]. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

Proposed def: A leaf that is borne on a stem.

Comment:

current part_of children of vascular leaf

Terms that are probably okay (only occur in vascular leaves):

• auricle - ok

• bundle sheath - ok

• leaf abscission zone - ok

• leaf collar - ok

• leaf vascular system - ok

• ligule - ok

• petiole - ok

• stipule - ok

• leaf intercalary meristem - probably ok - does it ever occur in non-vascular leaves?

• leaf sheath - probably ok - does it ever occur in non-vascular leaves?

(see part_of children of leaf)

Terms I'm not sure about:

• leaf aerenchyma- is there ever aerenchyma in non-vascular leaves?

• leaf mesophyll - should probably be part of leaf. Is there a mesophyll in non-vascular leaves?

Terms that should be part of leaf:

• leaf lamina - should be part_of leaf

• leaf margin - should be part_of leaf

• leaf base and leaf apex are already part of leaf (rather than vascular leaf)

Question from sharon.lewis@syngenta.com to Pankaj:Re: changing name of "leaf" to "vascular leaf"

> We are just updating our internal copies of some ontologies, and noticed some changes in the Plant Structure ontology from the Plant Ontology Consortium. (As you know we also use the Trait Ontology.) >

> We don’t so much like the change of “leaf” to “vascular leaf” for several reasons. If we use “vascular leaf” in an alphabetically ordered pulldown menu, users will miss it if they’re looking for leaf. Could you use “leaf, vascular” instead?

> I think I understand why the increased granularity was added in this area. (Sort of – if mosses aren’t really plants, why does the POC care about them?) I understand that the old “leaf” really meant leaf of a vascular plant, and the new “leaf” is supposed to mean something else.

> It causes search problems for us when a term is added that is the same term as a previous one, but with a different code. Do you know how others handle this situation?

Physcomitrella terms:

See Terms requested by Physco group for a list of terms.

Completion of Physco items from last week's agenda

Fill in here if any items from last week require further discussion

New items for Physco

Shoot apical meristem/apical cell

Apical development in bryophytes

Whole plant structures

These structures could either be is_a whole plant, or could be considered life-cycle phases (part of gametophytic phase). Need to decide how to handle them.

All definitions below are from Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary

protonema - The filamentous stage of gametophyte development. Protonemal tissue is produced following spore germination or the regeneration of most tissues (whether gametophytic or sporophytic). In most moss species, protonemal filaments comprise two cell types, caulonema (q.v.) and chloronema (q.v.). Both types of filament extend by the serial division of their apical cells. Sub-apical cells may branch.

Protonemata may develop from a spore or from a fragment of gametophytic tissue.

chloronema - The assimilitory filaments of the protonemal stage of gametophyte development. Compared to caulonmeal filaments, the cells of P. patens chloronemal filaments contain many well developed chloroplasts. The cross walls of adjacent cells in chloronemal filaments are perpenicular to the filament axis.

caulonema - The adventitious filaments of the protonemal stage of gemtophyte development. Compared to chloronemal filaments, the cells of P. Patnes caulonemal filaments contain only fewer, less well developed chloroplasts. The cross walls of adjacent cells in caulonemal filaments are oblique to the filament axis.

Collective plant structures

gametophore bud - A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove

gametophore - The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Actually, the gametophore is only the leafy part of the gametophyte, minus the protonema

perigynium/perigonium

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, wing and keel

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

The Phenotype Ontology RCN

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

ICBO

CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: The deadline for workshop and tutorial proposals for the ICBO conference is February 1, 2011

- We decided we are too shorthanded to put togehter 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

* 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.

See IBC 2011 Bio-Ontologies Symposium wiki page

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. Still waiting for abstract from Rudi Appels, who will speak on crop genomics and phenomics.

We received permission to use the 6th time slot for a discussion session. PJ will lead the discussion.