Report from the 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.

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.

vascular and non-vascular leaf

*non-vascular leaf: (PO:0025075)

Def'n: A leaf in a non-vascular plant. [source: POC:curators] Comment: Include moss and liverwort leaves. Occurs in the gametophytic phase of a plant life cycle.

Synonyms: exact: gametophyte leaf

- ok as is - Physco group has asked us to add phyllid as exact synonym. Can also add gametophyll as exact synonym.

*vascular leaf: (PO:0009025) Def'n: A leaf in a vascular plant. [source: POC:curators]

Synonyms: related: foliage leaf

Comment:In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud (APweb Glossary). Occurs in the sporophytic phase of a plant life cycle.

- ok as is - Suggest adding frond and needle as exact synonyms of vascular leaf.

Suggest adding scale-like leaf as a narrow synonym of vascular leaf. See: http://oregonstate.edu/trees/conifer_genera/false_cedars.html

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.

Will need to consider if the definition of epidermis works bryophytes (see section on Physco terms on next week's agenda).

leaf endodermis -- Does not occur in non-vascular leaves. This should probably be part_of vascular leaf, not leaf.

current is_a children of vascular leaf

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

juvenile leaf (PO:0006339)

Def'n: Distinct from adult leaves, being characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.

transition leaf (PO:0008018),

Def'n: A leaf that is part of an heteroblastic series, and is characterized by anatomical features that are intermediate between juvenile and adult leaves.

adult leaf (PO:0006340)

Def'n: Adult leaves are characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.

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 normally 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 the terms below (as phenotype terms)? At one point we discussed getting rid of them.

simple leaf (PO:0020042) Def'n: A leaf in which the lamina is undivided.

compound leaf (PO:0020043) Def'n: A leaf having two or more distinct leaflets that are evident as such from early in development.

Terms that are probably okay as children of vascular leaf:

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 define as bracts)

Current def'n: 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.

Suggest we flag this definition for later, but not deal with it for now, and leave it as is_a vascular leaf.

current part_of children of vascular leaf

(see part_of children of leaf)

Terms that 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? Normal growth in non-vascular leaves if from the tip.

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

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?

I (RW) haven't found any examples of the use of leaf aerenchyma or leaf mesophyll in leaves of bryophytes. Probably okay to leave them as children of vascular leaf.

From MAG: I did a search and I could not find any references on the presence or absence of aerenchyma in non-vascular leaves. It seems that they all should have some type of "mesophyll", since they have at least one layer of parenchyma and they photosynthesizes (for example Amblystegium and Funaria). Although they do not developed "vascular bundles" they can have some sort of midrib composed of conductive elements.

Terms that are part of vascular leaf but 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)

Do we keep these terms for vascular leaf and rename them, move them to non-vascular leaf, or obsolete them and create new children of leaf?

Physcomitrella terms:

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

-This was identified as a priority, since if we can get their terms in by the next release, they will use PO instead of continuing to develop their own ontology.

The Moss Ontology (MO) has about 65 PSO terms. About 20 of those already exist or are trival to add to the PO (e.g. non-vascular leaf base, non-vascular leaf apex). Many of the terms will be fairly straight-forward to add, but some will require discussion.

They have requested about about 35 PGDSO terms. About 10 of those already exist. The others should be fairly easy to add once the PGDSO is restructured.

Do we want to give MO/Physco terms their own number space? Maybe a subset of the NYBG number space.

Collective plant structures:

gametophore

Def'n supplied by MO: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia).

Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Suggest is_a shoot system.

Proposed def'n.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase

Comment: A gametophore is the leafy part of a moss gametophyte, without the protonema. Antheridia and archegonia arise on the gametophore.

gametophore bud

The term "bud" has been requested: Def'n supplied by MO: 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.

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A bud on a protonema that develops into a gametophore. participates_in gametophytic phase

Comment: Occurs in mosses.

Plant organs:

cauloid

- This is the term used for the gametophore stem or axis.

Suggest using gametophore axis as primary name, cauloid as synonym.

Proposed def'n: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase

Synonyms: cauloid, gametophyte axis

Also suggest adding terms for gametophore stem and gametophore branch (similar to stem and branch).

perigonial bract

- The specialized phyllids surrounding the antheridia.

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.

Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase

Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.

Additional moss terms:

These were not requested by the Physcomitrella group, but are commonly used to describe mosses, so we may as well add them now.

perichaetal bract

Proposed def'n: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.

Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.

gametophytic perianth

Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on an axis that are fused laterally and surround the calyptra.

Should it be surrounds the capsule, in case no calyptra is present?

-has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)

Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

seta

-The stalk of a moss sporophyte.

Suggested def'n: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

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.

Gametangium, antheridium, archegonium

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

Publications

Paper for ICBO meeting

-suggestion from BS, ICBO call for papers, (deadline is ~March 1st)

Could be expanded for submission to journal later- perhaps for the American Journal of Botany?

From 2-22: We will consider this if there is not too much overlap with the plan phys paper, as we don't want to jeopardize getting it published. Could focus more on the ontology aspects.

Special paper for American Journal of Botany

DWS contacted the editor of AJB, who felt that a special invited paper on the Plant Ontology would be a good idea. She asked for a target date.

Possible topics for the paper:

-What the PO is and why it is important to the readers of AJB (botanists and other plant scientists)

-How the PO unifies the study of plant sciences - cross-disciplinary studies

-Ontologies for systematics

-Examples/case studies: reproductive axes across land plant or seed plants, others?

Plant Physiology

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.

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

POC Conf. Call 3-1-11