POC Conf. Call 4-26-11

POC meeting, Webex Conference Call; Date: Tuesday Apr 26th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_4-19-11?

Issues arising from last week's meeting:

gametophytic phase and sporophytic phase

sporophytic phase (PO:0028002)

Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with fertilization or the division of a non-fertilized embryogenic cell.

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy or in vitro culture of haploid embryos.

gametophytic phase (PO:0028003)

Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]

Comment: During the gametophytic phase, a plant may produce gametes by mitosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with meiosis.

Comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory. This usually occurs when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.

embryonic plant structures

Definition of embryonic plant structure:

embryonic plant structure (PO:0025099):

At the POC_Conf._Call_4-19-11 we discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.

As a solution, we will specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations and develops from relations (e.g., seedling radicle develops_from embyronic radicle).

Proposed definition: A plant structure that is part of an embryo.

Comment: Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).

Terms that are is_a children of embryonic plant structure:

embryo proper (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.

scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.

suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from an embryonic basal cell and connects an embryo proper to the wall of a megagametophyte.

New definitions for embryonic plant cells and tissues

Both now have cross-product definitions, and no asserted is_a children

embryonic plant cell (PO:0025028): A plant cell that is part of an embryo.

is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo

Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion

Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)

Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.

(portion of) embryonic plant tissue (PO:0025233): A portion of plant tissue that is part of an embryo.

is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo

Should we add the portion of prefix to the name?

coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of embryonic plant tissue.

Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.

Here is a picture of some plant tissues, to show how it works:

Proposed changes/questions for structures that were is_a embryonic plant structure:

coleoptile (PO:0020033): A tubular (embryonic) plant structure developed at the junction of the cotyledonary sheath with the seedling axis, and surrounding the plumule of a monocot embryo or seedling. [APWeb:Glossary]

We do not have the term cotyledonary sheath in the PO, and, according to Beentje (the Kew Plant Glossary), the coleoptile is the cotyledonary sheath. Also, the coleoptile persists after germination, so it is not an embryonic plant structure. According to Esau, the coleoptile has stomata, which means it has an epidermis, and this consists of two or more tissue types. This makes it a plant organ, even though many authors casually refer to it as a tissue.

Proposed definition: A plant organ (phyllome?) that surrounds the plumule of an embryo or the emerging shoot apex of a seedling. [ISBN:9781842464229, ISBN: 0471244554]

Comment: Found in grasses. Develops at the first node above the scutellum, and thus is often thought to be the first leaf. Protects the emerging shoot system as it grows through the soil.

coleorhiza (PO:0020034): A portion of plant tissue surrounding the radicle in the embryo or seedling of some monocots. [APWeb:Glossary]

Currently part_of embryo, but it is also part of the seedling. It develops in the embryo, but persists after germination to protect the embryonic root. Suggest removing part_of plant embryo relation. The coleorhiza, like the coleoptile, has an epidermis (and root hairs), and thus should be classified as a plant organ, even though many authors casually refer to it as a tissue.

Proposed definition: A plant organ that surrounds the radicle in the embryo and seedling.

Comment: Found in grasses and some other monocots. Protects the emerging embryonic root.

hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]

currently is_a cardinal organ part, propose is_a stem internode (we didn't have this term before but do now)

Proposed definition: A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.

is_a stem internode

epicotyl (PO:0020035): The first internode of a stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. [APWeb:Glossary]

currently is_a embryonic plant structure, propose is_a stem internode (PO:0005005). Also, the second part of the current definition only adds ambiguity. Need to define it more precisely.

Proposed definition: The first stem internode above a hypocotyl. [Esau]

Comment: The epicotyl is the first internode of a stem above the cotyledons.

mesocotyl (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.

This definition sounds like the same thing as an epicotyl. Esau says the mesocotyl is the plant axis between the scutellum and the coleoptile and that in grasses, the scutellum is generally thought to represent the cotyledon and the coleoptile to represent the first leaf. In that case, the mesocotyl (as the axis between the scutellum and the coleoptile), is analogous (or homologous) to the epicotyl in dicots and other monocots. In grasses, the hypocotyl is not visible, except perhaps as the scutellar node.

For a picture, see http://www.agry.purdue.edu/ext/corn/news/timeless/GerminationEvents.html

Proposed definition: A shoot internode that is the part of an embryo axis or the stem of a seedling above the scutellum and below the coleoptile. [Easu]

Comment: Occurs in grasses. In grasses, the hypocotyl and cotyledon may not be visible and may be represented by the scutellar node and scutellum, making the mesocotyl similar to the epicotyl in other taxa. Elongation of the mesocotyl during seedling growth pushes the coleoptile above the soil surface.

hypocotyl-root junction PO:0004724: A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.

Moved to is_a cardinal organ part. Will automatically be is_a embryonic plant structure b/c it is part of embryonic axis. May want to remove this relation. The hypocotyl-root junction remains after germination. Or, perhaps we should keep it, because this structure is really only referred to during the embryonic phase.

Proposed definition: A cardinal organ part that is the part of a plant axis (or embryonic axis) where the radicle joins the hypocotyl.

Proposed synonym: transition zone (Bell and Bryan 2008, and others)

plumule(PO:0020032): A somewhat differentiated terminal bud in several embryo types above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.

made is_a terminal bud, part_of embryo

scutellar node (PO:0004708): The region in of an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached. [MaizeGDB:lv]

Sounds like it should be is_a stem node. Also, the region between the primary root and the plumule contains the mesocotyl as well as the scutellar node.

Proposed definition: A stem node that is the part of an embryo axis directly above the radicle where the scutellum is attached.

Comment: Found in grasses, where no hypocotyl is present. The scutellar node may represent a reduced hopocotyl and cotelydonary node.

is_a stem node, part_of embryo axis

embryonic root (PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]

Propose that this should be is_a root instead of is_a embryonic plant structure, b/c it is not necessarily part of an embryo.

Proposed definition: A root that is initiated in a developing embryo.

radicle (PO:0020031): The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive. is_a embryonic root [APWeb:Glossary]

Proposed definition: An embryonic root that is the basal continuation of a hypocotyl in an embryo and may develop into the root system of an adult plant.

Comment: Sometimes abortive.

remove part_of embryo axis, because it persists after germination.

embryonic leaf (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].

Is this an embryonic plant structure, that is, is it always part of the embryo?

Proposed definition: A vascular leaf that is one of the first few leaves to develop from the embryonic shoot apical meristem and is part of an embryo.

is_a vascular leaf,

Should this really be part_of embryo? Do these leaves persist after germination?

New terms for Physcomitrella and related taxa (continued)

Collective plant structures:

vascular and non-vascular shoot systems

The Moss Ontology did not request these terms, but we may want to add them in order to classify shoot systems.

non-vascular shoot system (PO:0030017): A shoot system that does not have as part vascular tissue.

comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.

subset for bryophytes

Could we use the relation "lacks_part"? Then we could define this class using intersection_of relations, which would be better. CL has used this (lack_plasma_membrane_part). Works better in OWL; translates into something like has_part exactly 0 (some Y).

Child of non-vascular shoot system will be gametophore (see below). A moss sporophyte could also be called a non-vascular shoot system. If we used the lacks_part relation and intersection_of relations, we could make gameotophore a child of shoot system, and the reasoner would infer it was a non-vascular shoot system.

Can't use participates_in gametophytic phase, because the sporophyte of a bryophyte might also be considered a non-vascular shoot system.

vascular shoot system (PO:0030016): A shoot system that has as part vascular tissue.

comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.

participates_in sporophytic phase, has_part vascular system

If we accept these terms, suggest changing definitions of vascular leaf (PO:0009025) and non-vascular leaf (PO:0025075) to "A leaf that is part of a vascular/non-vascular shoot system. This would be better than the current definitions which reference their taxonomy (part of a vascular or non-vascular plant) and would help with reasoning.

root-bourne shoot system (PO:0004544) should be is_a vascular shoot system

gametophore (PO:0030018)

Definition supplied by Moss Ontology: 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.: A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.

participates_in gametophytic phase, develops_from gametophore bud

Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.

subset for bryophytes

gametophore bud (PO:0030026)

The term "bud" has been requested: Def'n supplied by Moss Ontology: 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 vegetative bud that develops into a gametophore.

Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.

participates_in gametophytic phase, has_part gametophore apical cell

synonym: brown bud

thallus (PO:0030027)

From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.

From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.

Saying a thallus is a gametophore implies that it is a shoot system and therefore a collective plant structure (CPS). As a CPS, it must have more that one organ. This is not true for a thallus (sometime they branch, so you could say they have multiple axes, but it is a stretch. Maybe better to classify it as a whole plant.

proposed def: A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.

Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.

Add prothallium as a broad synonym of thallus and as a narrow synonym of whole plant.

Other gametophyte terms

We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.

apical cell

Moss Ontology has requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.

Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.

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." The embryonic apical cell can also be found in non-angiosperms. Suggest obsoleting PO:0004000 and replacing it with the new termembryonic apical cell for clarity, and using the name apical cell for the general class of apical cells described below.

Definition of apical cell from Esau: The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.

Definition of apical cell from Crum: A single cell at the tip of a stem, leaf, leaf or other structure that divides repeatedly to form new cells; also known as an apical intial.

Is apical cell more consistent with meristematic cell (A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall) or with initial cell (A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body)? Probably meristematic cell, because the apical cell can give rise to more than two cells (because it can have three or four cutting faces).

Proposed def. of apical cell (PO:0030007): A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex, or thallus apex.

Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves or thalli). An apical cell maybe established upon germination of a spore or upon the first cell division of an embryo or later.

-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.

Suggested ontology structure for the children of apical cell:

The dotted lines represent relations inferred by the reasoner.

Includes two ways of classifying: by structure and by gametophyte/sporophyte. Structural relations are asserted as is_a relations. The relations to gametophyte or sporophyte are inferred by the intersection_of terms.

New terms and definitions for apical cells

gametophytic apical cell (PO:0030014): An apical cell that is part of a whole plant in the gametophytic phase.

Comment: Occurs bryophytes and pteridophytes.

intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase

sporophytic apical cell (PO:0030015): An apical cell that is part of a whole plant in the sporophytic phase.

Comment: Occurs in pteridophytes and the sporophyte of bryophytes.

intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase

thallus apical cell (PO:0030025): An apical cell that is part of a thallus.

part_of thallus

root apical cell (PO:0030008): A sporophytic apical cell that is part of a root apical meristem.

comment: Occurs in the sporophytic phase of pteridophytes.

part_of root apical meristem

shoot apical cell (PO:0030009): An apical cell that is part of a shoot system.

comment: May occur in shoot axes or leaves of bryophytes or ferns.

part_of shoot system

gametophore apical cell (PO:0030019): A shoot apical cell that is part of a gametophore.

comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.

intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore

leaf apical cell (PO:0030011): A shoot apical cell that is part of a leaf apex.

comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some ferns. Only in plants where leaf growth is apical.

part_of leaf

non-vascular leaf apical cell (PO:0030013): A leaf apical cell that is part of a leaf apex of a non-vascular leaf.

comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.

part_of non-vasucular leaf; synonym: phyllid apical cell

vascular leaf apical cell (PO:0030012): A leaf apical cell that is part of the leaf apex of a vascular leaf.

comment: Occurs in vascular leaves of some ferns in their sporophytic phase.

part_of vascular leaf

shoot axis apical cell (PO:0030010): An apical cell at the tip of a shoot apical meristem.

Comment: Divides to produces leaf initial cells and other stem tissues.

part_of shoot apical meristem

gametophore axis apical cell (PO:0030023): A shoot axis apical cell at the tip of a gametophore axis.

Comment: Occurs at the tips of the stems and branches of bryophytes.

part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell

vascular shoot axis apical cell (PO:0030024): A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.

Comment: Occurs in some ferns in their sporophytic phase.

part_of vascular_shoot system; synonym: fern shoot axis apical cell

Also:

embryonic apical cell (PO:0025284, replaces PO:0004000): An apical cell that is part of an embryo and is the uppermost cell formed after the first division of a zygote.

Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain meristematic throughout the plant's life.