POC Conf. Call 4-19-11

POC meeting, Webex Conference Call; Date: Tuesday Apr 19th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_4-12-11?

New terms for Physcomitrella and related taxa (continued)

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 shoot axis that is part of a gametophore.

Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.

intersection_of: is_a plant axis, intersection_of: part_of gametophore

Add caulome as synonym of shoot axis

-Also suggest adding terms for gametophore stem and gametophore branch.

gametophore stem: A stem that is part of a gametophore.

is_a stem, part_of gametophore

gametophore branch: A branch that is part of a gametophore.

is_a branch, part_of gametophore

-If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or 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.

foot

Moss Ontology definition: The base of the sporophytes in mosses

Proposed name and def.: sporophyte foot: A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore. (ref: Schofeld)

Comment: Found in bryophytes and some pteridophytes. In mosses, the foot is located below the seta. In ferns, the foot is formed from the upper hypobasal quandrant of the embryo. The sporophyte foot serves for both attachment and absorption. The outer portion of the foot is composed of absorptive transfer cells. (ref: Crum)

participates_in sporophytic phase, has_part transfer cell, only_in_taxon bryophytes (I know this isn't a clade, will have to create a pseudo-clade).

Additional organ related moss terms:

These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we should add them now.

perichaetal bract

Proposed def'n: A bract that subtends an archegonium. part_of gametophore

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 a gametophore axis and surround the calyptra (capsule?).

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

-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)

Comment: The parachaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

seta

-The stalk of a moss sporophyte.

Proposed def.: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Comment: Found in some bryophytes, especially mosses.

antheridiophore and archegoniophore

These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)

Proposed definitions:

antheridiophore: A plant axis that bears two or more antheridia.

participates_in gametophytic phase

Comment: Found in Marchantiales.

archegoniophore: A plant axis that bears two or more archegonia.

participates_in gametophytic phase

Comment: Found in Marchantiales.

Will also add terms for antheridium stalk and archegonium stalk for stalks that hold up a single antheridium or archegonium. part_of antheridium or archegonium

Cardinal organ parts

Terms requested by MO:

• calyptra

Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.

We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named perianth calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.

Proposed name and def.: spore capsule calyptra: A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.

Comment: Found in bryophytes and pteridophytes (according to Parihar). The calyptra ia a membranous or hairy cap or hood composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.

participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?

subsets for bryophytes, pteridophytes

[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77

• venter

This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.

part_of archegonium

subsets for bryophytes, pteridophytes, gymnosperms

• archegonium neck

This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the elongated apica part of an archegonium.

Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

part_of archegonium

(can also add term for neck canal cell when we deal with cells)

subsets for bryophytes, pteridophytes, gymnosperms

• base

Proposed name and def.: sporangium base: A cardinal organ part that is the basal part of a sporangium.

Comment: Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)

part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis

subsets for bryophytes

• theca

Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that anther theca and call this term sporangium theca:.

Proposed name and def.: sporangium theca: A cardinal organ part that is the main body of a sporangium and has spores located in it.

Comment: Term used in mosses and other bryophytes (what about pteridophytes?)

part_of sporangium

subsets for bryophytes, maybe pteridophytes

• peristome

Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

proposed definition: A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.

Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.

part_of sporangium

subsets for bryophytes

• peristome tooth

Not requested by Moss Ontology, but should add it.

Proposed def: A cardinal organ part that is a single lobe or tooth of a peristome.

Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.

part_of peristome

subsets for bryophytes

• Add term for peristome cell? Are they dead at maturity? What kind of cells are they?

• lid/operculum

Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.

We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.

Proposed name and def.: spore capsule operculum: A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.

Comment: Found in mosses. May remain partly attached to the rest of the capsule.

Synonym: sporangium lid

part_of sporangium

subsets for bryophytes

Also add these terms for angiosperms:

fruit operculum: A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. apical part of a circumsesile fruit. part_of fruit

The top part of the bud where the perianth (petals) is fused. Leaves fruit underneath it. Operculum is underneath that

Comment: Found in Eucalyptus.

Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?

perianth calyptra: A collective plant structures that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.

Comment: Found in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit.

Other related terms for mosses, not from Moss Ontology

• spore capsule mouth

Proposed definition: A plant anatomical space that is the opening on the apical end of a spore capsule.

Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.

part_of sporangium

subsets for bryophytes

• epiphragm

Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."

From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."

Proposed definition: A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.

Comment: Present in some moss species of the family Polytrichaceae.

Synonym: tympanum, epiphram

subsets for bryophytes

• pseudopodium

From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."

From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."

Proposed definition: A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.

Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.

participates_in gametophytic phase

subsets for bryophytes

Sporangium

We currently have the class sporangium (PO:0025094), which is a cardinal organ part.

In bryophytes, the sporangium is a plant organ. In seed plants, it is a cardinal organ part (part of a sporophyll). In ferns, it grows on the surface of a leaf. Would it be legitimate to say that in seed plants, the sporangium is a reduced organ that is located in another organ?

Current def: A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]

Comment: May be multicellular or unicellular. In bryophytes, particularly in mosses, a sporangium is referred to as a capsule

We also have:

megasporangium (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]

microsporangium (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]

nucellus (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]

Comment: In seed plants, the megaspores and megagametophyte are retained within the nucellus.

pollen sac (PO:0025277): A microsporangium that is part of a sporophyll where the pollen grains developed and are contained after they develop. [source: POC:curators]

Comment: A pollen sac is a microsporangium in seed plants. In angiosperms, a single, unfused pollen sac may contain an anther locule or several pollen sacs may fuse so they contain a single anther locule.

Proposed def. nucellus: A megasporangium in a seed plant, composed of fleshy subepidermal tissue located in an ovule and surrounding a megasporocyte.

Proposed def. pollen sac: A microsporangium that is located in a sporophyll and where the pollen grains developed and are located after they develop. [source: POC:curators]

(comments stay the same)

We could continue to use the more general part_of relation for located_in

Sporangium parts

This is continued from our discussion at the POC_Conf._Call_3-8-11

Currently classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002). However, these layers and their constituent cell types can be part of any sporangium, not just an anther. Proposed making them part of a general class sporangium wall (as we did for parts of leaf).

From Smith:

Liverworts: Embryo divides to form outer layer (ampithecium) that gives rise to jacket layer and inner mass (endothecium) that gives rise to archesporium (cells of which divide to produce sporocytes and nurse cell, may also produce elators).

Hornworts: Embryo divides to form ampithecium that gives rise to jacket layer and primiary sporogenous layer, and endothecium that gives rise to sterile columella in all but one species (where it gives rise to sporagenous tissue). Jacket layer is 4-6 cells thick, and outer layer develops into epidermis. Sporagenous tissue gives rise to sporocytes and filaments of sterile cells called pseudoelators.

Sphagnum: Upper tier of cells in the embryo divides to form endothecium that gives rise to sterile columella and ampithecium that gives rise to outer sterile layer and inner archesporium. Archesporium gives rise to sporogenous layer two to four cells thick. Outer sterile layer gives rise to jacket layer 3 or 4 cells thick.

Eubrya: Early division of capsule gives rise to multilayered ampithecium and endothecium (with ampithecial cells and endothecial cells). Endothecium (usually) gives rise to archesporium and columella. Columella cells adjacent to archesporium remain small and develop into inner spore sac. Ampithecium develops into a multilayered structure, including layers with and without chloroplasts and an epidermis.

Psilophyta: Paired sporangia (a synangium or maybe a reduced sporangiophore) develop from a single cell. First cell division leads to a jacket initial and an archesporial (primary sporogenous) cell. Repeated periclinal divisions of jacket initial lead to jacket layer four or five cells thick and divisions of archesporial cell lead to many sporogenous cells. No tapetum develops. Near maturity, irregular clumps of sporogenous tissue divide to give rise to spore mother cells, remainder disintegrate

Lycopods: Sporangia borne on sporophylls.

Plant Cells

Terms requested by MO:

archesporial cell

We have the terms:

female archesporial cell (PO:0006015): In the majority of flowering plants including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]

male archesporial cell (PO:0006014): It undergoes periclinal divisions, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]

Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.

Proposed definitions:

archesporial cell A plant cell that gives rise to a sporocyte.

Comment: May be part of an archesporium.

female archesporial cell (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.

Comment: Found in heterosporous ferns and seed plants. In the majority of flowering plants, including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]

male archesporial cell (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.

Comment: Male archesporial cell may undergo periclinal division, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]

brachycyte

chloronema cell - done

caulonema cell - done

Other cell types, not requested by MO:

hyrdoid

leptoid

rhizoid initial

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.

Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.

Proposed definition: A plant organ/portion of plant tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.

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

midrib/costa

Moss Ontology definition: The nerve of a phyllid. Altered from Bill and Nancy Malcolm (2006)

We have term midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary] (which, by the way, should just say phyllome, instead of leaf or leaf-like organ). However, midvein is_a leaf vein, which is a portion of vascular tissue, so it cannot apply to mosses.

We should have a term that groups conductive tissue together for both vascular and non-vascular plants, kind of like we have axial cell for vascular and non-vascular conductive cells.

New child of portion of plant tissue: portion of axial tissue:

(also, we need to redefine phloem to be more like definition of xylem, and not based on function) (need to redefine axial cell so it doesn't say vascular cell)

rhizoid

archesporium

amphithecium

endothecium

jacket layer

paraphysis

axilliary hair

tmema

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."

Proppsed 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 bristle: A stipule that has a brush-like appearance.

Alternative is to suggest bristled to PATO

phyllode

Proppsed 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'

Proppsed 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'

Proppsed 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.

TraitNet requests

corm

proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.

child of stem (PO:0009047).

podarium

Their comment: is synonym to Tubercle

podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.

tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).

proposed def:

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.

diaspore

definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.

We could add this term as a kind of upper level bin term (similar to trichome)

cone

Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?

sorus

from Crum (2001): a cluster of fern sporangia from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.

Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.

Part_of vascular leaf, has_part sporangium

tendril

Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.

tendrils can derived from multiple types of structures. Suggest we make separate terms:

branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.

leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.

Can add other types of tendrils if they come up or users need them.

root terms

submitted by Rich Zobel (Nov 2009)

User requests still open on Source Forge; PGDSO

tuber growth and development stages

This item has been open on SF since 6/2009

I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).

Suggested stages:

-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)

-tuber initiation

-tuber growth

-tuber maturation

How we work these in will depend on restructuring of PGDSO

l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926

terms for seed development stages

This is a fairly new request for terms for cotton