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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

Luctenbergia

root terms

Submitted by Rich Zobel (Nov 2009).

Still need to work on definitions for these terms.

User requests still open on Source Forge; PGDSO

coleoptile emergence

This was dealt with 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.

terms for seed trichome development stages

Open since 07-28-2010

Request

The following terms have been requested for cotton fiber development (their structure and defintions):

seed development stages PO: 0001170

---[part_of]Seed hair development stages

---[part_of]seed hair initiation stage: The earliest histological evidence of seed hair initiation, ie, a change in the orientation of cell division in the ovule epidermises occurs at or just before anthesis. (Ruan YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].

---[part_of]seed hair elongation stage: A period of rapid elongation of hair initials without cell division for 16-25 days. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources:PMID: 17905721, PMID: 12671090].

---[part_of] seed hair secondary wall biosynthesis stage: A phase of the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

---[part_of]seed hair maturation stage: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA). (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

Question: are they more interested in this as a seed development stage or as a trichome development stage?

Existing terms and definitions:

seed development stages (PO:0001170)

Current definition: Stages of seed development, from fertilization to the dry or quiescent state. [source: TAIR:ki]

Proposed name and definition: seed development stage: A plant structure development stage that begins with fertilization and ends with seed maturation.

Comment: Only used for seed plants. Some seeds may enter a period of dormancy after seed development is complete.

is_a plant structure development stage; part_of sporophyte phase; subset for gymnosperms and angiosperms; add relation: seed participates_in seed development stage

leaf trichome development stage (PO:0007039): Stages of development of a trichome defined by characteristic morphological, structural, histological or other visible features.

is_a leaf development stage

New terms and proposed definitions:

seed trichome development stage: A plant structure development stage that is part of a seed development stage during which one or more seed trichomes develop.

is_a plant structure development stage; part_of seed development stage; add seed trichome participates_in seed trichome development stage

synonym: seed hair development stage

seed trichome initiation stage: The earliest histological evidence of seed hair initiation, ie, a change in the orientation of cell division in the ovule epidermises occurs at or just before anthesis. (Ruan YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].

synonym: seed hair initiation stage

seed trichome elongation stage: A period of rapid elongation of hair initials without cell division for 16-25 days. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources:PMID: 17905721, PMID: 12671090].

synonym: seed hair elongation stage

seed trichome secondary wall biosynthesis stage: A phase of the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

synonym: seed hair secondary wall biosynthesis stage

seed trichome maturation stage: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA). (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

synonym: seed hair maturation stage

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

Conductive cells and tissues for vascular and non-vascular plants

THIS PART IS STILL UNDER CONSTRUCTION

conductive tissue types

trace as possible name for category for veins, central strands, and costas

vascular tissue

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 may occur 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)

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 tube members.

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

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 phloem tissue that is the part of a primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

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

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

xylem

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

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

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 or phloem. May also contain other types of tissue such as plant fibers, vascular cambium, or portions of ground tissue.

part_of vascular system

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, surrounding the hilum that forms a groove in the surface of the pericarp immediately adjacent to the hilum.

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

plant fibers - new tissue types

portion of plant fiber: Currently fibers are plant cell types, but they should also be a tissue type.

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

Comment: Contains elongated, lignified fiber cells that are dead at maturity.

phloem fiber: A portion of plant fiber that has as parts phloem fiber cells.

xylem fiber: A portion of plant fiber that has as parts xylem fiber cells.

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

This term only applies to vascular leaves, and should be renamed vascular leaf vein.

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

part_of leaf vascular system, part_of leaf lamina

• Suggest new term primary leaf vein: A vascular 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.

• 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". Suggest we rename it vascular leaf midvein to distinguish it from costa.

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

Comment: Often the most prominent vein of a vascular leaf.

broad synonyms: mid rib, midrib, mid-rib

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

• Moss Ontology has requested the term midrib for bryophytes. It is often called a costa.

Proposed definition for costa:' A central strand that is part of a non-vascular leaf.

Comment: Found in bryophytes, especially mosses.

part_of non-vascular leaf

broad synonyms: mid rib, midrib, mid-rib

Refs:

Sperry 2003, IJPS; Hebant 1977;

conductive and related cell types

See also conducting cells for non-vascular plants.

Current parent: axial cell

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.

Existing descendents of axial cell:

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)

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

At the bryophyte term meeting on 4-25-2011 (RW and MAG present), we decided that axial cell was not the correct term to use to describe all of the elongated cells associated with conducting tissue in plants. They are different cell types and have different origins, so they should not all be grouped together.

New proposed hierarchy (children of plant cell):

plant cell

>hydroid

>leptoid

>vascular cell (new term)

>>sieve tube member

>>tracheary element

>>>tracheid

>>>vessel member

>>phloem fiber cell

>>xylem fiber cell

>>other kinds of fiber cells

>ground tissue cell (PO:0025030)

>>stereid

>>collenchyma cell

>>sclerenchyma cell (PO:0000077)

>>>fiber cell (new term)

>>>sclerid (new term)

Proposed definitions:

fiber cell:

vascular cell:

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.