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User requests open on Source Forge: PAO

Legume terms

submitted by Austin Mast

Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)

See agenda for 7-05-2011.

Remaining:

banner, wing and keel

These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 Sunday_Sept_11th,_2011

phyllode

This item is on the agenda for POC_Conf._Call_9-20-11

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.

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.

TraitNet requests

podarium

Their comment: is synonym to tubercle (but it isn't exactly the same)

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 enlarged modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).

[This article] describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:

"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."

proposed def. podarium or tubercle: under construction

corm

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

child of stem (PO:0009047).

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.

Comment: Pneumatophores are found in trees that live in flooded habitats such as mangroves. May provide oxygen to below ground roots growing in flooded soils.

tendril

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

tendrils can be (evolutionarily) 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 and lacks a lamina. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.

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

This is the way we defined spine (no parent class spine, only leaf spine and stipule spine with is_a relations to leaf and stipule).

Alternative is to create a parent 'tendril'(is_a plant structure) with children that are part_of the other structures:

tendril: A plant structure that is slender and coiling. Comment: Aids plant in climbing.

branch tendril is_a tendril part_of branch

leaf tendril is_a tendril part_of leaf

leaflet tendril is_a tendril part_of leaflet

leaf apex tendril is_a tendril part_of leaf apex

The part_of relations are technically correct (not proper part), but I don't think it conveys the proper meaning. Also, according to the formal definitions, a leaflet tendril or a leaf apex tendril would be a leaf tendril as well.

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

Synonym of strobilus (PO:0025083) or child?

proposed def: A strobilus that is woody?

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

root terms

Submitted by Rich Zobel (Nov 2009).

Still need to work on definitions for these terms.

New children of calyptra perianth

This item is on the agenda for POC_Conf._Call_9-20-11.

User requests still open on Source Forge; PGDSO

from MaizeGDB:

See discussion of these items on POC Conf. Call 8-30-11

---

coleoptile emergence -- definition

These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 Sunday_Sept_11th,_2011

This item is on the agenda for POC_Conf._Call_9-20-11.

5 fruit formation; FF.00 fruit size 10%

These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 Sunday_Sept_11th,_2011

This item is on the agenda for POC_Conf._Call_9-20-11.

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].

Suggested terms and definitions:

Do we want to use stage or phase throughout PGDSO?

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

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 for bryophytes and vascular plants

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 make it a child of the new class portion of axial tissue (see below), and also 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)

currently part_of vascular bundle. Removed this relation, because it is not true for all plants. Also vascular bundle is now a portion of vascular tissue, so it can't be part_of.

children of vascular tissue:

hydathode (PO:0005660) - A structural modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis. [GR:pj, ISBN:0080374913]

Should be is_a cardinal organ part. Do hydathodes ever occur on stems or branches, or are they always part of phyllomes?

proposed definition: A cardinal organ part that releases water through a pore.

Comment: Usually found on leaves. Hydathodes may have one or more pores that appear to be incompletely developed stomata that lack the ability to open and close. Generally, hydathodes are located at the end of a minor vein. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.

leaf vein (PO:0005417) - see more below details below

phloem (PO:0005417): 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): 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): The first-formed elements of the primary phloem.

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

tracheid bar (PO:0019026): 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]

-should be is_a xylem

xylem (PO:0005352): A portion of vascular tissue composed of (that has as parts) xylem elements.

vascular bundle (PO:0005020): 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 or vascular cambium. May also contain portions of ground tissue.

part_of vascular system

New children of plant tissue:

hydrome: A portion of axial tissue that has as parts hyrdoids.

Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in water conduction and support, similar to xylem in vascular plants.

Synonyms: hydrom, leptoxylem (Hebant)

leptome: A portion of axial tissue that has as parts leptoids.

Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.

Synonyms: leptom, leptophloem (Hebant)

central strand: A unit strand of axial tissue that has as part hydrome or leptome.

Comment: Often contains both hydrome and leptome. Found in bryophytes located in the center of non-vascular shoot axes such as a gametophore axis or seta, or in the costa of a non-vascular leaf.

synonyms: conducting strand, central cylinder

stereome: A portion of axial tissue that has as parts stereids.

Comment: Found in bryophytes.

From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.

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

Proposed definition: A portion axial 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): 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 for bryophytes and vascular plants

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: