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

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

This would be is_a root and would be separate from the existing term tuber (PO:0004543). PO:0004543 should probably be renamed shoot tuber, but its definition is okay. Can add comment that shoot tubers can be distinguished by scale-like leaves and/or axillary buds. Root tubers can often be distinguished by have lateral roots or their remnants. Sometime root tubers have vegetative buds on them like shoot tubers, but these arise from adventitious 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