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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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.

Open items from older agendas and user requests

Primordium

primordium (PO:0025127), current def.: 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.

At previous meetings, there was a discussion of making this a subtype of plant organ, but we decided it was better as portion of meristem tissue (can have as parts different types of meristem tissue).

proposed def.: A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and ground meristem (PO:id) and is committed to the development of a particular plant structure.

Comment: A primordium appears as a protrusion and develops in to a plant structure such as a phyllome (PO:0006001) or anther (PO:0009066). The transition from primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.

Need to look at which tissue form first. Maybe epidermis.

ground meristem

We don't actually have a term for ground meristem. Propose that we add one.

Esau says "A primary meristem or meristematic tissue, derived from the apical meristem and giving rise to ground tissues." However, the ground meristem can also give rise to procambium, which gives rise to vascular tissue.

ground meristem (new term), proposed def.: A portion of meristem tissue (PO:0009013) that develops from an apical meristem (PO:0020144) and ...

subtypes of primordium

CPS: anther, gynoecium (seems like if we are going to have gynoecium, we should have androecium), flower (will obsolete)

COP: lodicule (should also add leaflet)

Organ: root, including later root and adventitious root; phyllome, including carpel, cotyledon, leaf, petal, sepal, stamen

Other: abaxial side of leaf primodordium, adaxial side of leaf primordium

Currentlly, each type of primordium is defined as "as primordium will develop into an xxxx". However, it might be better to say "is committed to the development of xxx", or something like that.

floral organ primordium (new term): A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395).

comment: A floral organ primordium may develop into a carpel, petal, sepal, or stamen.

Add carpel, petal, sepal, and stamen primordium as subtypes. Will have dual parentage.

If we want to include anther primordium and gynoecium primordium here, then we need to call it "floral structure primordium".

floral structure primordium (alternative term and definitions): A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) or other floral structure such as a gynoecium (PO:0009062) or anther (PO:0009066).

Other types of primordia, proposed definition: A primordium (PO:0025127) that is committed to the development of a anther/gynoecium/lodicule/phyllome/etc.

Proposed definitions and comments for specific types of primordia:

root primordium (PO:0005029: A primordium (PO:0025127) that is committed to the development of a root (PO:0009005).

Comment: Root primordia may arise from pericycle cells (PO:0025261), as in most seed plants, cells of an endodermis (PO:0000252), as in ferns, or from cells on a shoot axis (PO:0025029), in the case of basal root primordia and shoot-borne root primordia. Transition from root primordium to root occurs when formation of a root apical meristem and root cap begins.

lateral root primordium (PO:0000016): A root primordium (PO:0005029) that is committed to the development of a lateral root (O:0009005).

comment: A lateral root primordium generally develop from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in the formation of a lateral root primordium in some species, and in ferns lateral root primordia develop from the endodermis. Transition from lateral root primordium to lateral root occurs when formation of a root apical meristem and root cap begins, which can occur before the lateral root penetrates the exterior of the parent root.

adventitious root primordium (PO:0008038): A root primordium (PO:0005029) that is committed to the development of a basal root (PO:0025002) or a shoot-borne root (PO:0000042).

We don't actually have a term for adventitious root, so it would be better to obsolete this term and add new terms for basal root primordium and shoot-borne root primordium. There are no annotations on adventitious root primordium. Same goes for adventitious root apical meristem (PO:0006021) and adventitious root epidermis (PO:0006039).

ovule primordium: When integuments form?

leaf primordium, current def.: 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."

leaf: when ab/adaxial meristems start to form - works for other phyllomes too.

Even though we don't have a PO term for it, people also use the term "leaflet primordium", which is also a cardinal organ part. (We have a term for formation of leaflet primordium).

anlagen

We have terms for root anlagen, phyllome anlagen, carpel anlagen, leaf anlagen, and cotyledon anlagen. We have develops_from relations between leaf, carpel, and cotyledon primordia and their respective anlagen. Suggest adding similar relations for phyllome and root.

misc. notes

Note: leaf marginal meristem is part_of leaf primordium and part_of vascular leaf. Can't be both, unless leaf primordium is a leaf, which it isn't. Same for phyllome marginal meristem.

Note: promeristem should be a synonym of AM, not RAM.

ovule

current def. of ovule (PO:0020003): A stalked or sessile structure in a seed plant within which one or more megaspores are formed and later the female gametophyte or embryo sac develops.

At the POC meeting on 4-17-12, we agreed to make ovule a plant organ, instead of a cardinal organ part. It may be part of carpel, which is a plant organ, but we already have other examples of organs that are part of other organs (e.g., nucellus and pollen sac).

Also, ovule is currently part_of ovary, but that is only true for angiosperms. Ovules can be found in all seed plants.

From Fahn: A structure (in a seed plant) consisting of the nucellus which contains the female gametophyte, one or two integuments, and the funiculus.

proposed def.: A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) containing a female gametophyte (PO:0025279), one or two integuments (PO:0020021), and a funicle (PO:0020006), but does not have as part an ovary (PO:0009072).

comment: A seed develops from an ovule. In angiosperms, an ovule is located in an ovary.

RW: I don't really like the wording of the last part, but I put it in there to distinguish it from carpel, which is also a plant organ that has as parts a nucellus containing a female gametophyte , one or two integuments, and a funicle.

PJ requested separate subtypes for ovarian ovule vs non-ovarian ovule, to make annotation easier.

There is nothing special to distinguish a non-ovarian ovule, so we could do like we did for sporangium, and have a specific subtypes for ovarian ovule, but just classify other types of ovules as ovule.

If we add a term for ovarian ovule, then we also need subtypes for the parts of the ovule in an ovary (antiraphe, chalaza, integument, nucellus, raphe).

Alternatively, we could add ovary has_part ovule, then put a comment on ovule, antiraphe, chalaza, integument, nucellus, and raphe to add an additional annotation to ovary, as we did for leaf.

root tuber

Propose adding a new term for root tuber. This is the structure found in cassava and Ipomoea (sweet potato).

proposed def., root tuber: An enlarged storage root.

Comment: Root tubers often develop from shoot-borne roots (). Root tubers may be distinguished from shoot tubers by the presences of a root cap () when very young or the presence of lateral roots () or their remnants. Sometime root tubers bear vegetative buds like shoot tubers, but these arise from adventitious buds or are derived from the stem to which the shoot-borne root is attached.

Refs.: Bell and Bryan, ISBN:978088192850. See also: Cassava of Tropical Africa, ISBN:9781310413

This would be is_a root and would be separate from the existing term tuber (PO:0004543).

Suggest renaming PO:0004543 (and its subtypes) shoot tuber. Its definition is okay. Add comment that shoot tubers can be distinguished from root tubers by the presence of scale-like leaves and/or axillary buds.

lobe and tooth

Need to update SF tracker based on discussion with MAG on ~4-2-12.:

add comment that lobes can have teeth

difference is not pointed or round, but size

A tooth is general - serra pointed, crinna rounded AJB Hickey 1974, Blicher 1973 Bot Review toothed margin means it is not entire. sinus can be angular or rounded, depending on type of teeth.

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.

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. part_of phyllome margin

proposed definition, plant organ lobe: A cardinal organ part that is a rounded projection on the margin of an organ.

part_of lamina

Should this really be part of the margin? The margin is defined as "the edge of an organ and the area immediately internally adjacent to it".

proposed definition, phyllome lobe: A lobe that is a rounded projection on the margin of a phyllome.

part_of phyllome margin

proposed definition, leaf lamina lobe: A phyllome lobe that is a rounded projection on the margin of a leaf lamina.

part_of leaf lamina margin

Should this be in vascular leaf only?

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, phyllome 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? - no)

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.

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