Items In Progress
This page is a place holder for us to put items that will be scheduled for discussion at upcoming meetings.
Topics will move off of here as they are dealt with.
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User requests still open on Source Forge: PSO
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.
bristle
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
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.
User requests still open on Source Forge; PGDSO
Maize GDB
IL.03 full infloresecence length reached
Add two related synonyms:
3.4 late vegetative (maize)
VT (maize)
Also add to the comment: In US cornbelt maize, the tassel fully emerges about 2-3 days prior to silk emergence from husk leaves. At this time the ear and husk may still be enclosed within its leaf sheath depending on the variety and environmental conditions.
LP.18 eighteen leaves visible
Under synonyms add: related: VT vegetative transition in maize (US cornbelt)
3 infloresence visible - rework the tree, add a term
Current structure:
From Mary: Humble suggestions for reworking this part of the ontology so that very early stages of all species can be lumped, and to make it easier to annotate.
(1) “PO:0007047 3 inflorescence visible” should be redefined to include early stages where it may be visible (eg booting) but not yet emerged. One might rename the visible to ‘detectable’ and define appropriately.
current definition: The stage at which plant is producing inflorescence(s). is_a B reproductive growth
proposed definition, 3 inflorescence detectable phase: A reproductive growth phase during which one or more inflorescences is detectable.
Comment: This includes the time when inflorescence may be developing (e.g. booting in Zea) but not yet emerged. Includes times when inflorescences are detectable only by assay or with a microscope.
(2) PO:0007006 IL.00 inflorescence just visible should include the booting stage, etc. Perhaps rename to - IL.00 inflorescence just detectable. This will permit lumping with similar stages in Arabidopsis for example. Basically, all the developmental programs are in place and the structure is growing, even if only visible as a bulge in the sheath, or by stripping off the vegetative parts to view.
RW: What Mary describes is still visible (if the structure is actually growing), with manipulation of the plant or aid of a microscope. Use of the word detectable includes times when it could be detected by assay, but not visible. I think if we want a phase that describes that, we should add a separate phase: "inflorescence just detectable", for times when the inflorescence can be detect, but not seen, but only if people need it.
current definition: Inflorescence just visible to the naked eye.
proposed definition, IL.00 inflorescence just visible phase: An inflorescence detectable phase during which one or more inflorescences is just visible to the naked eye but not yet developed.
Comment: Includes the time when the inflorescence can be seen by removing outer leaves or bracts, or when the inflorescence is detectable as a swelling of the outer leaves or bracts, such as booting in Zea.
(3) PO:00070411 inflorescence emergence from flag leaf sheath would now have a direct is_a relationship with ‘3 inflorescence visible’.
Additional comment from Mary: "the term 'emergence from flag leaf sheath' be made more global and be called something like inflorescence emergence (eg from flag leaf sheath, from leaf sheath) with appropriate definition. This way all terms save 2 (per above) would be retained."
current definition, inflorescence emergence from flag leaf sheath: The stage at which the inflorescence emerges from the flag leaf sheath.
proposed definition, inflorescence emergence phase: An inflorescence visible phase during which an inflorescence emerges from sheathing leaves or bracts.
Comment: Includes emergence of a Zea inflorescence from a flag leaf.
(4) PO:0007014 booting would be merged to the term PO:0007006 inflorescence just detectable.
Suggest merging PO:0007014 booting with PO:0007006 IL.00 inflorescence just visible phase. All children of booting would stay under booting.
(5) Obsolete PO:0007012 Poaceae inflorescence visible as would no longer be required.
Suggest merging PO:0007012 into inflorescence detectable stage, rather than obsoleting it. Descendents of PO:0007012 (booting and inflorescence emergence from flag leaf sheath) are already moved to other parents, see above.
coleoptile emergence -- definition
From Mary at 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.
PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."
All of the sibling terms to cotyledon emergence (coleoptile, epidcotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.
Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?
PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleteling the term and creating a new one.
Adding the replaced_by link would make moving existing annotations straightforward. There are 133 annotations on shoot emergence, including 1 from coleoptile emergence and 2 from cotyledon emergence.
Also, all of these terms should be renamed as stages or phases rather than as developmental processes - so, for example, PO:0007045 should be called coleoptile emergence stage, rather than coleoptile emergence. The definitions should reflect the fact that they are stages, not processes.
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. We should fix these while we're redefining the terms.
current structure:
current: seedling growth: Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination
Seedling growth stage should probably begin after germination, not after imbibition.
proposed: A vegetative growth phase that begins with germination and ends with the development of the first adult leaves.
Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
current: shoot emergence: Shoot or leaf breaks through the soil surface.
proposed: shoot emergence phase: A vegetative growth phase that occurs when a shoot system emerges from a seed.
current:
proposed:
current:
proposed:
current:
proposed:
current:
proposed:
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;
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:
