Items In Progress

This page is a place holder for us to put items that will be scheduled for discussion at upcoming meetings.

Please include the date when the item was added; topics will move off of here as they are dealt with.

-Go back to POC_Meetings_Minutes main page

User requests open on Source Forge; PDSO

terms for seed trichome development stages

Requests for terms for cotton fiber development, Open since 07-28-2010, from AgBase curators

These items are on the agenda for POC_Conf._Call_11-15-11 and POC_Conf._Call_11-22-11.

coleoptile emergence

This was discussed at the NYBG Meeting, on Sunday_Sept_11th,_2011

We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed. (rather than above ground)

This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.

At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.

Comment: This terms is used only for seed plants.

proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.

Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???

Comment: This terms is used only for seed plants.

proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???

Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.

current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence from growth medium development stage (PO:0007049): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

proposed: cotyledon emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.

current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence from growth medium development stage (PO:0007054): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.

proposed: epicotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.

current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence from growth medium development stage (PO:0007043): A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

proposed: hypocotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.

Could also add terms for feeder emergence for some gymnosperms.

For all of the above terms, need to check existing synonyms and move or copy them as needed.

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

User requests open on Source Forge: PAO

notes:

other terms for cacti: glochid and areole

spinule: word for when the spines are stipules – synonym of stipule spine

root terms

Submitted by Rich Zobel (Nov 2009).

Still need to work on definitions for these terms.

Conductive cells and tissues for vascular and non-vascular plants

THIS PART IS STILL UNDER CONSTRUCTION

vascular tissue types

For vascular plants, we have the class:

portion of vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]

Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.

part_of vascular bundle (which is part_of vascular system)

This is okay, but suggest that we change definition to include xylem or phloem.

Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve tube members.

Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissue, such as fibers.

part_of vascular system (should add vascular system participates_in sporophytic phase)

vascular bundle (PO:0005020) current def.: A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]

This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.

proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.

Comment: Usually contains both xylem and phloem. May also contain other types of tissue such as plant fibers, vascular cambium, or portions of ground tissue.

part_of vascular system

add vein as exact synonym -- can be in any organ

phloem

phloem (PO:0005417) current def.: A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]

proposed definition: A portion of vascular tissue that has as parts sieve elements.

Comment: Functions in the conduction of organic substances in vascular plants.

Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.

metaphloem (PO:0006076) current def.: Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

proposed definition: A portion of primary phloem that differentiates after the protophloem.

Comment: Differentiates before the secondary phloem, if any is formed.

protophloem (PO:0006077) current def.: The first-formed elements of the primary phloem.

proposed definition: A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.

primary phloem (PO:0006075) current def.: A portion of phloem tissue of the primary plant body.

proposed definition: A portion of phloem tissue that develops from the procambium.

Comment: Primary phloem develops as part of GO:xxxx primary growth. (see below)

develops_from PO:0025275 procambium

secondary phloem (PO:0005043) current def.: A portion of phloem tissue formed by the activity of the vascular cambium.

proposed definition: A portion of phloem tissue that develops from the vascular cambium.

Comment: Secondary phloem develops as part of GO:0080117 secondary growth.

develops_from PO:0005598 vascular cambium

proposed terms for GO

definitions from Esau (ISBN:0471245208 or 9780471245209)

Are these types of GO:growth (The increase in size or mass of an entire organism, a part of an organism or a cell.) or GO:developmental process (A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.)

primary growth (new terms):

proposed definition: A type of growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed.

comment: Has its inception in the apical meristems and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously.

is_a growth (GO:0040007)

secondary growth (GO:0080117):

Current definition: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290

Proposed definition: A type of growth of a stem or root, characterized by an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium.

Comment: Occurs in vascular plants (including gymnosperms and most dicots). Commonly supplemented by activity of the cork cambium (phellogen) forming a phelloderm. Primary and secondary growth can occur simultaneously. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth.

xylem

xylem (PO:0005352) current def.: A portion of vascular tissue composed of xylem elements.

comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.

proposed definition: A portion of vascular tissue that has as parts tracheary elements.

comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.

primary xylem (PO:0005849) current def.: A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194]

Comment: In stem or root it is differentiated behind the apical meristem.

proposed definition: A portion of xylem tissue that differentiates from the procambium.

Comment: Primary xylem develops as part of GO:xxxx primary growth.

develops_from PO:0025275 procambium

protoxylem (PO:0000272) current def.: A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208]

proposed definition: A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.

metaxylem (PO:0000372) current def.: A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208]

proposed definition: A portion of primary xylem that differentiates after the protoxylem.

Comment: Differentiates before the secondary xylem, if any is formed.

secondary xylem (PO:0005848) current def.: A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]

Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.

Existing definition is okay.

New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed o secondary xylem.

develops_from PO:0005598 vascular cambium

Note: exarch, endarch, mesarch are descriptors for different types of xylem development.

tracheid bar (PO:0019026) current def.: A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]

proposed definition: A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.

Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]

part_of seed; adjacent_to hilum

leaf vein, midrib, costa

• leaf vein (PO:0020138), current def: A strand of vascular tissue in the leaf blade.

is_a portion of vascular tissue; part_of leaf vascular system

proposed definition, leaf vein (PO:0020138): A vascular bundle that is part of a leaf lamina in a vascular leaf.

part_of leaf vascular system, part_of leaf lamina

synonym: leaf vascular bundle

Suggest new term primary leaf vein: A leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.

Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).

• midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]

Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.

proposed definition: A primary leaf vein that is the central vein of a vascular leaf.

Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf.

broad synonyms: mid rib, midrib, mid-rib, vascular leaf midvein

related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128

We already have terms for secondary, tertiary, quaternary, and higher order veins.

plant fibers - new tissue types

Currently fibers are plant cell types. Do we need fiber as a tissue type too?

Proposed definition, portion of plant fiber: A portion plant tissue that has as parts fiber cells.

Comment: Contains elongated, lignified fiber cells that are dead at maturity. May function in strengthening and support the plant.

conductive and related cell types

under costruction

See new vascular cell types.

Current parent: axial cell

Existing structure:

axial cell (PO:0000081)

>sieve tube member (PO:0000289, alt: PO:0000286)

>phloem fiber (PO:0004519)

>xylem element (PO:0000273)

>>tracheary element (PO:0000273)

>>>tracheid (PO:0000301)

>>>vessel member (PO:0002003)

>>xylem fiber (PO:0000274)

>>>fiber tracheid (PO:0000355)

>>>libriform fiber (PO:0004520)

>>>septate fiber (PO:0004521)

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]

Comment: These cells make up the axial system, also known as vertical or longitudinal system.

The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.

New tissue terms:

secondary vascular tissue: A portion of vascular tissue that develops from the vascular cambium. (ref: Esau)

comment: Forms as part of secondary growth (GO:xxxx) in vascular plants. May contain both tracheary elements and sieve elements, plus other types of ground tissue cells. Differentiated into the axial system and ray system.

If we set this up as a cross product, then secondary xylem and phloem will be inferred children of it.

axial system: A portion of secondary vascular tissue that has as parts cells derived from the fusiform cambial initials and oriented with their longest diameter parallel to a root or shoot axis.

synonyms: vertical system, longitudinal system

ray: A portion of secondary vascular tissue that has as parts tracheary elements or sieve elements that develop from ray initials.

comment: Of variable width and height. Extends radially in the secondary xylem and phloem of a plant axis

ray system: A portion of secondary vascular tissue that has as parts all of the rays in a plant structure.

comment: May refer to the ray system of a shoot axis, a root, or an entire plant.

synonyms: radial system, horizontal system

New proposed hierarchy (children of plant cell):

plant cell

>sieve element (new term)

>>sieve tube member (syn.: sieve tube element)

>>sieve cell (new term)

>tracheary element

>>tracheid

>>vessel member

>ground tissue cell (PO:0025030)

>>sclerenchyma cell (PO:0000077)

>>>sclerid (new term)

>>>fiber cell (new term)

>>>>phloem fiber cell

>>>>xylem fiber cell

>>>>other kinds of fiber cells?

New definitions

Definitions from Esau's Anatomy of Seed Plants

sieve element (new term)

proposed def.:

sieve tube member (PO:0000289)

current def.: One of the series of cells that make up a sieve tube; it shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores).

comment:Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.

proposed def.:

syn.: sieve tube element

sieve cell (new term)

proposed def.:

xylem element (PO:0000273): A cell making up xylem tissue.

Currently, this is parent of tracheary element and xylem fiber. I suggest we obsolete it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber.

tracheary element (PO:0000290)

current def.: General term for any water conducting cell, tracheid or vessel member.

proposed def.:

tracheid (PO:0000301)

current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.

proposed def.:

vessel member (PO:0002003)

current def.: One of the cellular components of a vessel, a dead cell with the wall between adjacent members being variously perforated and the walls that persist variously thickened.

proposed def.:

sclerenchyma cell (PO:0000077)

current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.

proposed def.:

sclerid (new term)

proposed def.:

fiber cell (new term)

proposed def.:

phloem fiber cell (PO:0004519) (was called phloem fiber)

current def.: A fiber in phloem.

proposed def.:

xylem fiber cell (PO:0000274) (was called xylem fiber)

current def.: A fiber in xylem.

proposed def.:

fiber tracheid (PO:0000355): A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.

libriform fiber (PO:0004520): A xylem fiber commonly with thick walls and simple pits.

septate fiber (PO:0004521): A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.

other kinds of fiber cells?

other wood terms

Wood is a synonym for secondary xylem (PO:0005848) -- see definition above.

axial wood parenchyma ; PO:0004533: Parenchyma tissue in the axial system of secondary xylem.

axial wood parenchyma cell ; PO:0004526 Parenchyma cell in the axial system of secondary xylem. plant anatomy early wood ; PO:0004515 The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.

heartwood ; PO:0004512 The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.

late wood ; PO:0004516 The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.

procumbent wood ray parenchyma cell ; PO:0004529 Ray cell within secondary xylem having its longest axis in radial direction.

ray wood parenchyma ; PO:0004534 Radially oriented parenchyma tissue in secondary xylem.

ray wood parenchyma cell ; PO:0004527 Parenchyma cell of a ray in secondary xylem.

sapwood ; PO:0004513 Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.

upright wood ray parenchyma cell ; PO:0004528 Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.

wood parenchyma ; PO:0004532 Parenchymatous tissue occurring in the wood.

wood parenchyma cell ; PO:0004525 Parenchyma cell occurring within secondary xylem.

wood parenchyma is_a secondary xylem. Should be is_a parenchyma.

wood parenchyma (PO:0000272) current def.: Parenchymatous tissue occurring in the wood. [source: POC:Curators]

proposed definition:

Legume terms

All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.

bristle

(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)

Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.

At the POC meeting on 9-27-11, it was decided that bristled stipules should best be handled as a phenotype term. Leaving these notes here for when we start to add phenotypic descriptors.

We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.

A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).

There are two meanings for bristled:

!. Stiff and sharp (e.g., a bristled trichome)

2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)

Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):

1. bristle-like:

This is a combination of two PATO descriptors:

Something describing the shape:

PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.

or

PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.

and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.

and something describing a quality of a substance:

PATO has:

PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)

PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)

A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.

PATO:

quality of a substance (existing)

>flexibility (existing)

>>flexible (existing)

>>inflexible (existing)

>rigidity (new)

>>rigid (new)

>>flacid (new)

2. bristle-bearing: A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.

is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)

Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).

To describe legume stipules, we may also need a term brush-like: A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.

Then if we want to, we could add terms like brush-like stipule (is_a stipule) or bristle-like stipule (is_a stipule) or bristle-bearing stipule, or users could post-compose these terms on their own.