POC Conf. Call 3-1-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 1st, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_2-22-11?

Report from the 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.

Physco terms

Term requested by MO that are already in PO but need some work

epidermis (PO:0005679)

Current def: A portion of plant tissue composed of epidermal cells that develops from the protoderm and covers the surface of a plant structure. [source: POC:curators].

Comment: The epidermis can be composed of one or more layers of cells. In some species, the epidermis is replaced by periderm. Epidermis can also include trichomes and stomatal pores (add root hairs and rhizoids too).

Is there a protoderm in non-vascular plants? (def: A portion of meristem tissue that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.)

phyllid base and phyllid apex

We already have the terms leaf base (PO:0020040) and leaf apex (PO:0020137). The choice is to make phyllid base (=non-vascular leaf base) and phyllid apex (=non-vascular leaf apex) synonyms of these terms, or to make them is_a children (see discussion of part_of children of leaf, above).

The same issue also applies for phyllid trichome/leaf trichome.

spore capsule

We have the term moss capsule (PO:0025232), but having a taxon name in the term name is not desirable, nor is having it defined based on its taxa. Suggest renaming it spore capsule and defining it based on its unique characteristics.

Current definition: A sporangium in mosses.

Proposed def.: A sporangium...

Comment: Found in mosses.

transfer cell

We have the term transfer cell (PO:0000078). Def: A cell with wall ingrowths (or invaginations) that increase the surface of the plasmalemma. [source: ISBN:0471245208] Comment: Appears to be specialized for short-distance transfer of solutes.

MO suggested definition: Specialized cell at the junction of the gametophyte and sporophyte that function in nourishing the sporophyte. [source: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition]

Are transfer cells always at the junction between the sporophyte and gametophyte? Do we want to include that in the definition or in a comment?

Do we want to add a specialized term for transfer cells in mosses? Are they different from other transfer cells?

Basal endosperm transfer cell (PO:0009018) is currently the only is_a child of transfer cell.

New items for Physco

Shoot apical meristem/apical cell/phyllome

MO has requested the term apical cell.

We already have the term apical cell (PO:0004000), which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." Suggest renaming PO:0004000 "embryonic apical cell" for clarity. The embryonic apical cell can also be found in non-angiosperms.

Growth in mosses (and other bryophytes?) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. Mosses do not have an apical meristem in the same sense as vascular plants.

If we define apical cell as is_a meristematic cell, we will have a problem. Even though apical cell is consistent with the definition of meristematic cell (synthesizing protoplasm and producing new cells by division and with only a primary cell wall), it is not consistent with the relation meristematic cell part_of meristem. A meristem is a portion of tissue and therefore two or more cells. We could solve this problem by changing meristematic cell part_of meristem to meristem has_part meristematic cell.

Proposed def. of apical cell: A meristematic cell at the apex of a gametophore or non-vascular leaf (phyllid).

Comment: Occurs in mosses and other bryophytes.

Apical cells also cause an issue with or definition of phyllome (PO:0006001): "A lateral plant organ produced by a shoot apical meristem." This definition is not strictly applicable to non-vascular leaves, which are phyllomes. Suggest we tweak the definition of phyllome to allow for this.

Proposed def. of phyllome: A plant organ produced by the lateral portion of a shoot apex.

Comment: In vascular plants, phyllomes arise from the shoot apical meristem. In non-vascular plants, phyllomes arise from division of a sub-apical cell (sometimes referred to as a leaf initial).

Whole plant structures

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

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

The Physco group classified protonema as whole plant, but could be considered a life-cycle phase (part of gametophytic phase). Need to decide how to handle it. After the leafy part of the gametophyte develops from the protonema, the protonema still persists, so there is some part of the life cycle in which the protonema is not the whole plant.

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

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

The MO classified chloronema and caulonema as is_a protonema, therefore is_a whole plant, but maybe they could be considered portions of tissue. They also have terms for chloronema cell and caulonema cell, but those are pretty straight-forward.

Proposed definition of chloronema:

Proposed definition of caulonema:

Cardinal organ parts

Terms requested by MO:

calyptra

base

peristome

theca

lid

foot

neck canal

Other terms, not from MO

epiphram

spore capsule mouth

pseudopodium

venter

Plant Tissues

paraphyllium - Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."

Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.

MO has this listed as a plant organ

Proposed definition: A phyllome/portion of plant tissue that is a small filamentous, scale-like, or leaf-like outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves. Found in pleurocarpous mosses and a few leafy liverworts.

The paraphyllia are the small, dark structures between the leaves.

midrib

rhizoid

archesporium

amphithecium

endothecium

jacket layer

paraphysis

axilliary hair

tmema

Plant Cells

Terms requested by MO:

archesporial cell

apical cell

shoot apical cell

phyllid apical cell

alar cell

brachycyte

chloronema cell

caulonema cell

tmema cell

jacket layer cell

axillary hair terminal cell

axillary hair base cell

neck canal cell

side branch initial

Other terms, not requested by MO:

hyrdoid

leptoid

rhizoid initial

Upcoming meetings 2011:

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: 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.

Next meeting scheduled for Tues, Mar. 8th, 2011 at 10am PST

See IBC 2011 Bio-Ontologies Symposium wiki page for more details