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.
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Unfinished items from older agendas and user requests
lobe and tooth
On 1-10-12, we added the term "sinus" and agreed to add the related terms for tooth and lobe, all part_of some margin.
We currently have organ margin (PO:0025005), phyllome margin (PO:0025018) without part of relations. Suggest that we add organ margin is part_of lamina, phyllome margin part_of phyllome lamina.
Leaf margin (PO:0020128) is already part of leaf and leaf lamina margin (PO:0025009) is part_of leaf lamina.
proposed definition, lobe: A cardinal organ part that is a rounded projection on the margin of an organ.
part_of organ margin
proposed definition, phyllome lobe: A lobe that is a rounded projection on the margin of a phyllome.
part_of leaf phyllome margin
proposed definition, leaf lamina lobe: A phyllome lobe that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)
part_of leaf lamina margin
can add other types of lobes as we want, or wait until they are requested.
proposed definition, plant organ tooth: A cardinal organ part that is a pointed projection on the margin of an organ.
part_of organ margin
proposed definition, phyllom tooth: A plant organ tooth that is a pointed projection on the margin of a phyllome.
part_of leaf phyllome margin
proposed definition, leaf lamina tooth: A phyllome tooth that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)
part_of leaf lamina margin
can add other types of teeth as we want, or wait until they are requested.
Be sure to add "teeth" as exact plural synonym to all.
Ref.: Harris and Harris, ISBN:0964022168.
bud areole and lamina areole
At the POC meeting on 11-8-11 we to add a term for areole, refering to a type of bud in cacti. However, this term is also used to refer to a part of a leaf (or other phyllome) lamina.
Proposed definition, bud areole (PO:0025353): An axillary bud that does not elongate, in which the leaves develop as spine leaves.
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
is_a axillary bud
ref.: Bell and Bryan, ISBN:9780881928501
Suggest we add a general term for lamina areole, which will cover petals, etc., and a more specific term for leaf lamina areole.
Proposed definition for lamina areole (PO:0025391): A cardinal organ part that is the smallest part of a lamina that is completely surrounded by veins. Comment: Any order of vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a lamina. part_of lamina
Proposed definition for leaf lamina areole (PO:0025392): A lamina areole that is the smallest part of a leaf lamina that is completely surrounded by leaf veins. Comment: Any order of leaf vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina
Ref: ISBN:9780801475184
colony/ramet/genet
This is a request from Daniel, with the Physco group.
"The description of moss phenotypes in many cases is at the level of (clonal) colony instead of single plant (which is IMO hard to define in this case). E.g. people measure colony area, diameter, branching etc. I want to annotate phenotypes using the EQ model by linking to PATO terms."
Suggest we add the following synonyms:
to "gametophore" (PO:0030018) narrow synonym: "ramet"
to "whole plant" (PO:0000003) related synonym: "ramet", narrow synonyms: "colony", "clonal colony", "genet"
On a related note, Daniel added that "IMHO plant growth/life forms should be best integrated as an extension to PO. "
Primordia
These issues came up while we were working on new term requests for Agron-Omics.
primordium (PO:0025127): A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]
Comment: The primordium is the first distinct form in the development of a plant structure.
leaf primordium: A phyllome primordium that will develop into a leaf. [source: POC:Curators]
Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).
I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.
"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."
General question: Do these tissues only occur in the primordium, or continue on after it becomes a young leaf? When does it stop being a primordium? If these tissues are all part of LP, then presumably the LP ends when cell stop dividing. I think usually the term primordium is used for the earliest stage of an organ's development, not all the way up until cell division ceases. Maybe better to say they develop from LP and are part_of leaf during PO:0001052 leaf expansion stage.
We felt primordium should probably be an organ. All primordia have at least two types of tissue - protoderm and ground meristem(?).
Primordium ends and leaf begins with the formation of the different meristems (adaxial, plate) that contribute to the final form of a leaf.
Problem with having different types of primordia as organs means they will all have dual parentage (is_a primordium and is_a whatever type of organ. We were trying to get rid of that when we made it is_a tissue.
promeristem as synonym of AM, not RAM
User requests open on Source Forge; PSDS
from MaizeGDB:
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
From Naama Menda: 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 PSDS
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
User requests open on Source Forge: PAO
Cacti terms:
spinule: word for when the spines are stipules – synonym of stipule spine
In Beentje, spinule is defined as a small spine. Could be narrow synonym for stipule spine and other kinds of spines
areole
Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
is_a axillary bud
ref.: Bell and Bryan, Plant Form
glochid
cladode and phylloclade
From Beentje:
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
proposed definition:
cladode: A shoot axis that is flattened and expanded.
comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.
synonyms: phylloclade, cladophyll
Need to open a SF tracker for these
Should also add 'rib' for cacti and other plants
root terms
Submitted by Rich Zobel (Nov 2009).
Still need to work on definitions for these terms.
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.
New Annotation Files
Strawberry
- Strawberry is on SVN: strawberry
Potato Annotations
LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.
From Dr. Richard Finker (Wageningen, The Netherlands):
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
This will go in the next release, do they have expression data- RNA Seq?
Annotation Guidelines
Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR
-This will also be helpful when applying for new grants
-it would be helpful to have a detailed guide on our wiki for collaborators
