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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To-do list for July 2012 Release

-new multi-tissue structures and CPS still say LC:test, change to POC:curators done

• typo in comment

-fix definition hilum groove, open tracker -Done. Already on tracker for parts of seed.

-fix annotations on flower primordium done

-pericarp on emergence terms Added as a comment to seed emergence terms.

-update definitions and comments of upper level terms with PO ids and new names done

- have new icon for located_in;

Add to icons for relations done

needs to be updated on wiki: Relations_in_the_Plant_Ontology and in AmiGO browser in progress done

see embryo sac (PO:0025074)

-fix comment on plant egg cell: see SF tracker RW: Looks like this is already done.

- Update the webpages- which ones are top priority?

- move files to live tag, update /trunk/ontology/OBO_format/Readme.txt

For next release:

- file naming and which variations of the file to create for each release - check with cjm

-caryopsis new child of fruit

-adventitious root nodule

Def'ns of former children of CPS need to be updated:

These are now children of CPOS

• PO:0009066 : anther
• PO:0009069 : anther theca
• PO:0025360 : ceonosorus
• PO:0025023 : collective phyllome structure
• PO:0025025 : root system
• PO:0009006 : shoot system
• PO:0025359 : sorus

other things to fix

• Minor typos in comment of multi-tissue plant structure, floral organ, def'n of bract

primordium

• Comment of primordium: A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), orncollective plant structure (PO:0025007).

This should read: A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or a collective plant organ structure (PO:0025007).

Or should it now refer to the new collective plant structure term: PO:0025497 (includes collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269)??

Types of primordia:

primordium; PO:0025127

>floral structure primordium; PO:0025477

No po term for "floral structure" but is defined as a plant structure that is part of a flower (PO:0009046),

such as a floral organ (PO:0025395), gynoecium (PO:0009062), or anther (PO:0009066) and is part of a reproductive shoot apex (PO:0025222).

Parts of flower:

floral organ: flower bract, petal, carpel etc; gynophore- shoot axis (plant organ) (note these all have dual inheritance)

portion of plant tissue: flower abscission zone, flower nectary, flower vascular system (is_a shoot system vascular system)

collective plant organ structure: anther, collective phyllome structures: androecium, gynoecium,

>leaflet primordium; PO:0025481 (is_a cardinal organ part)

>phyllome primordium; PO:0025128 (is_a plant organ)

>root primordium; PO:0005029 (is_a plant axis is_a plant organ)

terms for grapes and the ripening stages:

Anatomy terms

• fruit (PO:0009001):

narrow synonym: berry

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

add narrow synonym: grape berry skin

fruit storage parenchyma (PO:0025037): A portion of storage parenchyma that is part of a fruit.

add narrow synonym: grape berry flesh, grape berry pulp

• FF.04 fruit size 70% to final size stage (PO:0007027): A fruit formation stage that spans the interval when a fruit has reached 70% of its final size to its final size.

related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79

Add related synonym: BBCH principle growth stage 77; Berries beginning to touch

Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)

Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)

Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)

• FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.

Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour

Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison

• FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening

related synonym: BBCH principal growth stage 83

Add related synonym: middle of veraison

• FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.

related synonym: BBCH principal growth stage 89

Add related synonym: grape E-L stage: 38; Berries ripe for harvest

References:

Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 link

Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 link

BBCH grapes

generative cell (PO:0020097) and related terms

generative cell (PO:0020097) and related terms

We need to fix this definition, as it currently only includes angiosperms

Current def'n: generative cell (PO:0020097): A cell of the male gametophyte of angiosperms that divides to produce two male gametes or sperm cells. [source: APweb:Glossary]

Proposed def'n: A plant cell (PO:0009002) of the microgametophyte (PO:0025280) of seed plants that divides to produce two plant sperm cells (PO:0000084) in angiosperms and the the sterile cell (PO:xxxxxxx) and spermatogenous cell (PO:xxxxxxx) in gymnosperms.

Need to add to PO: sterile cell (PO:xxxxxxx) and spermatogenous cell (PO:xxxxxxx)

should be: part_of the microgametophyte (PO:0025280)

Definition from Raven 5th ed: generative cell: 1. In gymnosperms, the cell of the male gametophyte that divides to form the sterile and spermatogenous cells

2. In angiosperms, the cell of the male gametophyte that divides to form two sperm

Probably should also have the prothallial cell- part of the gymnosperm pollen grain: Definition from Raven 5th ed: The sterile cell or cells found in the male gametophytes, or microgametophytes of vascular plants other than angiosperms; believed to be the remnants of the vegetative tissue of the male gametophyte.

Generative cells can occur in both angiosperms and gymnosperms. They are the same thing, even though they develop into something else. Need to look at Singh's book on gymnosperm embryology.

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

we also have the term:

caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]

Problematic plant structures

specific problems

ovary and the like

An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.

The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).

ovary wall: Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.

style: (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.

If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.

stigma: Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.

anther and filament

Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this cool picture).

It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).

Stele

PO:0025197 : stele: A cardinal organ part that is the central column of a plant axis that consists of the primary vascular tissue and associated ground tissue. should be part -of plant axis? RW: Yes. Just add it.

Lamina

Make lamina is_a cardinal part of MTPS, add new term for organ lamina. Add logical definition for cardinal organ part, so organ lamina will be inferred child. Could also add shoot axis lamina, as sister to phyllome lamina.

tuberous root, continued

in progress

On further investigation, it seems that not only primary growth is involved in the formation of root tubers. There is secondary thickening from irregular growth from the vascular cambium, as well as thickening due to cell division in the cortex. Need to look into it more.

Also, it seems there are both tuberous roots (enlarged roots that form tubers along part of their length), and tubers, that form within those roots (see http://aob.oxfordjournals.org/content/38/2/307.full.pdf+html and hortsci.ashspublications.org/content/44/3/651.full.pdf)

ovuliferous scale

New term to add

"Ovuliferous scale" seems to be the more commonly used name.

proposed def., ovuliferous scale: A megasporophyll (PO:0009027) that is part of a seed-scale complex (add)

Comment: Has as part an ovuliferous scale ovule (add) and is part of an ovulate cone (add)

Should also work on definitions of megasporophyll and sporophyll.

New terms:

seed-scale complex: A repoductive shoot system (or inflorescence branch?) that is part of an ovuluate cone (or strobilous) and has as parts a ovuliferous scale and a sterile bract (need more precise name).

sterile bract: A bract that is part of a seed-scale complex and subtends an ovuliferous scale.

Wood ontology terms

See separate page: Wood Ontology PO and GO Term Development

Open items from older agendas and user requests

vegetative buds

This is ready to go on meeting agenda.

We have terms for axillary and terminal vegetative buds that are defined as developing into either a long or short shoot. This is not appropriate, because those are not the only things the buds can develop into, and the terminology "long shoot" and "short shoot" are not used in every taxon.

axillary vegetative bud (PO:0004712), current definition: An axillary bud that develops into a long or short shoot.

axillary vegetative bud (PO:0004712), proposed definition: An axillary bud (PO:0004712) that develops into a shoot system (PO:0009006) that has as organ parts only vegetative organs.

terminal vegetative bud (PO:0004716), current definition: A terminal bud that develops into a long or short shoot.

terminal vegetative bud (PO:0004716), proposed definition: A terminal bud (PO:0004713) that develops into a shoot system (PO:0009006) that has as organ parts only vegetative organs.

The new term, areole bud (PO:0025353), will be a subtype of axillary vegetative bud.

lobe and tooth

This is ready to go on meeting agenda.

References: AJB Hickey 1973 (http://www.jstor.org/stable/2441319), Dilcher 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

crenae

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

Recent interesting paper on cladodes in Asparagus:

Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. The Plant Cell Online, 24, 929 –940.

root terms

Submitted by Rich Zobel (Nov 2009).

Still need to work on definitions for these terms.

Leaf development stages

Current structure:

This seems pretty good, overall. Need to look into non-vascular leaf development and see if it applies there as well, or if we will need separate terms for vascular and non-vascular leaves.

new parent term

phyllome development stage, proposed def.: A plant organ development stage that has as primary participant a phyllome (PO:0006001).

Comment: Includes stages for the intitiation, expansion, and sensecence of a phyllome such as a leaf, lemma, or stamen.

lemma development stage (PO:0001047), lodicule development stage (PO:0001049), and palea development stage (PO:0001048), currently under flower development stage, should go here, and instead be part_of flower development stage.

Will also need a new term "bract development stage", parent to lemma and palea development stage.

leaf development stage

leaf development stage (PO:0001050), current def.: Stages of development of a leaf defined by characteristic morphological, structural, histological or other visible features.

proposed def.: A phyllome development stage (PO:id) that has as primary participant a leaf (PO:0025034).

Flower development stages

needs a lot more work than leaf stages

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