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

pericarp and seed coat

pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.

Synonyms related: fruit peel, fruit rind

endocarp ; PO:0009086, synonym inner epidermis of pericarp

exocarp ; PO:0009085 synonyms outer epidermis of pericarp,

http://en.wikipedia.org/wiki/Caryopsis

is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.

The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.

The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.

link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251

Open items from older agendas and user requests

ovule

Moved to POC Conf. Call 5-1-12

lobe and tooth

References: AJB Hickey 1973 (http://www.jstor.org/stable/2441319), Blicher 1973 Bot Review, Harris and Harris, ISBN:0964022168, also FNA glossary.

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.

Margins- part_of relations: 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.

phyllome sinus (existing definition): A plant anatomical space that is a phyllome marginal embayment, incision or indentation between marginal projections of any sort, typically lobes, teeth, or the base of cordate phyllomes. also have term for leaf sinus

Add comment that a sinus can be angular or rounded.

Lobes can be either rounded or pointed, and are defined based on the size of the projection.

Teeth' are pointed projections that extend less than 1/4 of the way to the midline.

Crenae (sing. crena) are small rounded pointed projections that extend less than 1/4 of the way to the midline.

lobes

proposed definition, phyllome lamina lobe: A cardinal organ part (PO:0025001) that is a projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends one quarter or more of the distance to the center of the long axis of the phyllome lamina (PO:0025396).

Comment: A phyllome lobe may be either rounded or angular at the tip, and may have phyllome teeth (PO:id) or phyllome crenae (PO:id) on its margin. The corresponding phyllome sinus may be rounded or angular.

part_of phyllome lamina (rather than part of lamina margin, because they lobe includes all of the tissue inside the margin).

proposed definition, leaf lamina lobe: A phyllome lobe (PO:id) that is a projection on a leaf lamina margin (PO:0025009) for which the corresponding leaf sinus (PO:0025384) extends one quarter or more of the distance to the center of the long axis of the leaf lamina (PO:0020039).

Comment: A leaf lobe may be either rounded or angular at the tip, and may have leaf teeth (PO:id) or leaf crenae (PO:id) on its margin. The corresponding leaf sinus may be rounded or angular.

part_of leaf lamina

Can add other types of lobes as needed.

ref: JSTOR:2441319

teeth

proposed definition, phyllome lamina tooth: A cardinal organ part (PO:0025001) that is an angular projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends less than one quarter of the distance to the center of the long axis of the phyllome lamina (PO:0025396).

Comment: See phyllome lamina crena (PO:id) for a small rounded projection. The corresponding phyllome sinus may be rounded or angular.

part_of phyllome lamina

proposed definition, leaf lamina tooth: A phyllome lamina tooth (PO:id) that is an angular projection on a leaf margin (PO:0020128) for which the corresponding leaf sinus (PO:0025384) extends less than one quarter of the distance to the center of the long axis of the leaf lamina (PO:0020039).

Comment: See leaf lamina crena (PO:id) for a small rounded projection. The corresponding leaf sinus may be rounded or angular.

part_of leaf lamina

Can add other types of teeth as needed.

Add "teeth" as exact plural synonym to all. Other synonyms from FNA.

ref: JSTOR:2441319

teeth

proposed definition, phyllome lamina crena: A cardinal organ part (PO:0025001) that is a rounded projection on a phyllome margin (PO:0025018) for which the corresponding phyllome sinus (PO:0025383) extends less than one quarter of the distance to the center of the long axis of the phyllome lamina (PO:0025396).

Comment: See phyllome lamina tooth (PO:id) for a small angular projection. The corresponding phyllome sinus may be rounded or angular.

part_of phyllome lamina

proposed definition, leaf lamina crena: A phyllome lamina crena (PO:id) that is a rounded projection on a leaf margin (PO:0020128) for which the corresponding leaf sinus (PO:0025384) extends less than one quarter of the distance to the center of the long axis of the leaf lamina (PO:0020039).

Comment: See leaf lamina tooth (PO:id) for a small angular projection. The corresponding leaf sinus may be rounded or angular.

part_of leaf lamina

Synonyms: scallop (exact), crenule (narrow)

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: Plant Anatomical Entities

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

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.

colony/ramet/genet

(Added ~3/23/2012) On a related note, Daniel added that "IMHO plant growth/life forms should be best integrated as an extension to PO. "

Also need acrocarpous and pleurocarpous moss (these could be growth forms).

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