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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Things To be fixed

Typo in the comment of multi-tissue plant structure.

Already fixed. See dev browser.

For 10-4-12 skype meeting

laticifer cell

From Dennis:

Articulated Laticifer: formed of a longitudinal series of cells with complete to perforated cross walls. Synonym- Compound Laticifer

Non-articulated Laticifer: single cells which may be coenocytic and branched and may grow intrusively but are not joined to form tubes. Synonym- laticifer cell or simple laticifer

Laticifer: cell or series of cells with latex, tubular and simple to branched.

laticifer cell (PO:0025031), current def.: A ground tissue cell that contains latex.

proposed definition: A tubular ground tissue cell (PO:0025030) that contains latex.

comment: May be simple or branched.

non-articulated laticifer cell (PO:0006222), current def.: A laticifer cell that elongates indefinitely and grows intrusively between the walls of meristematic cells.

Does it only grow between meristematic cells?

Proposed def: A laticifer cell (PO:0025031) that is not joined to other laticifer cells to form a tube.

Comment: May be coenocytic (multi-nucleate) and branched and may grow intrusively between other plant cells.

synonyn: simple laticifer

articulated laticifer cell (PO:0006221), current def.: A laticifer cell in which the walls between contiguous cells may partly or completely disappear.

Proposed def.: A laticifer cell (PO:0025031) that is joined longitudinally to other articulated laticifer cells to form a tube.

Comment: The walls between contiguous cells may be perforated or may disappear completely.

Non-articulated laticifers originate in the embryo from single celled laticifer primordial, and as development of the plant proceeds, the primordial grow longitudinally and symplastically with some apical intrusion and often extensive branching (Mahlberg, 1961).

synonym: compound laticifer cell

Articulated laticifers originate in the apical meristem as single cells, they growth preceeds are they increase in length acropetaylly by the addition of new cells without intrusive growth. Have non-lignified, primary walls.

articulated laticifer (new terms): A portion of ground tissue (PO:0025059) that has as parts articulated laticifer cells (PO:0006221).

Comment: The articulated laticifer cells are joined longitudinally to form a tube, with cross-walls that may be partially to fully perforated.

syn: portion of articulated laticifer tissue

embryo sac egg cell

The current definition says "A plant egg cell that is produced by and located in an embryo sac."

The embryo sac is not really a "sac" in which the egg cell is located. The embryo sac egg cell is located in the ovule, but we already can infer that, because the embryo sac is located in the ovule.

The phrase "produced by an embryo sac" is a bit odd, because the egg cell is part of the embryo sac, not produced by it. It develops as part of the embryo sac development, and we already have the relation "embryo sac develops_from megaspore". Also, we don't have a "produced by" relation in the PO.

I think a more appropriate definition for embryo sac egg cell would be:

A plant egg cell (PO:0020094) that is part of an egg apparatus (PO:0020096)

Comment. The egg apparatus is part of an embryo sac (PO:0025074).

We don't technically need that last phrase "that is part of an embryo sac (PO:0025074)", but I think it helps to clarify why this is called an embryo sac egg cell and not an egg apparatus egg cell. It could just go in the comment.

comment: An egg apparatus is part of an embyro sac (PO:0025074).

Update def. of embryo sac to say that it is located in a plant ovary ovule.

comment: has as part embryo sac egg cell

placenta

New term placenta (PO:0025078) was added in 7/2010, parent of ovary placenta and fruit placenta (which formerly had no is_a parent).

Current def.: A portion of plant tissue to which and ovule or seed is attached (Raven et al.).

I propose broadening the definition, as there can be other types of placentas (placentae?).

Proposed def.: A portion of plant tissue at the interface between two plant structures that are part of separate organisms and has as parts transfer cells (PO:0000078).

Comment: The transfer cells aid in nutrient transport. Examples include ovary placenta (PO:0020001) and fruit placenta (PO:0004535).

central cell

This comment was made by Paula Rudall during the beta review

Her comment: in a gymnosperm archegonium, the central cell is the cell that will divide to form the ventral canal cell and the egg cell (see Rudall 2006, Bioessays 28: 1067–1071). PMID:17041880

Dennis said: The gymnosperm definition is the older one and the one most commonly used.

Rename PO: 0020090 to embryo sac central cell.

Current def.: The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.

modified def.: An embryo sac cell (PO:0025026) that is largest cell in a mature embryo sac.

Comment: In most angiosperms, the embryo sac central cell contains two polar nuclei, and, after double fertilization, develops into an endosperm. In some angiosperms, such as Illicium, the embryo sac central cell contains a single polar nucleus. This is distinct from an archegonium central cell (PO:id).

New terms:

archegonium central cell

def.: A plant cell (PO:0009002) that is the larger, apical cell arising from the first division of an archegonial initial (PO:id) in a gymnosperm.

Comment: Divides asymmetrically to form a smaller archegonium neck canal cell (PO:0030065) and a larger archegonium egg cell (PO:0025122).

PMID:17041880

Add archegonium egg cell develops_from archegonium central cell.

archegonial initial: An initial cell that is part of an archegonium megagametophyte (PO:0025282) that divides to give rise to an archegonium (PO:0025126).

PMID:17041880

Related issue

megagametophyte cell (PO:0025026): A plant cell that is part of an embryo sac.

Should be renamed "embryo sac cell" and be defined using cross-products (is_a plant cell X part_of embryo sac)

spur

This term was requested by Elena Kramer during the beta review (with regards to Aquilegia, but can occur in other flowers).

defintion (from Beentje 2010): (in flowers) a slender hollow extension (usually) of the perianth, often containing nectar.

A spur may be either part of a petal or a perianth (multiple fused petals) I suppose it could occur in tepals too. Really, a spur could be on any phyllom, but we don't need to add them all until they are requested.

proposed term - petal spur: A cardinal organ part (PO:0025001) that is a slender, hollow extension of a petal (PO:0009032).

Comment: Often contains nectar. Use this term if the spur is part of a single petal. If the spur is part two or more fused petals, use corolla spur (PO:id).

proposed term - corolla spur: A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.

Comment: Often contains nectar. Use this term if the spur is part of two or more fused petals. If the spur is part of a single petal, use petal spur (PO:id).

Lamina

lamina (PO:0025060): A part of a plant structure that is thin and flat.

Currently is_a cardinal organ part, but there can be laminae on non-organ structures, such as seeds or fruits.

proposed def.: A cardinal part of multi-tissue plant structure (PO:0025498) that is thin and flat.

Already has child phyllome lamina. Maybe add intermediate term organ lamina.

Could also add a term for shoot axis lamina, as sister to phyllome lamina.

Note: Make cardinal organ part XP of is_a cardinal part of MTPS and part_of plant organ, so organ lamina will show up there.

lobe and tooth

We have already discussed this. Just need to update SF and the dev file.

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)

root tuber

current name and def.:

tuberous root (PO:0025476): A radially enlarged root (PO:0009005).

comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuberous roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuberous root is attached. A tuberous root usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).

Add "root tuber" as exact synonym.

Cacti terms:

not ready yet - for next week

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.

ovuliferous scale

not ready yet - for next week

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.

To-do list for July 2012 Release

- 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

other things to fix

• ovary wall should not be a cardinal organ part as ovary is not an organ See Items_for_future_meetings#ovary_and_the_like below.
• pappus element should not be a COP, as a pappus is not an organ- collective organ part structure. Each pappus element is a part of some organ (although there is some debate about which organ it is part of), thus pappus element is a cardinal organ part. The pappus is a collection of pappus elements, and therefor a collective organ part structure. I think the classification is correct.
• egg apparatus- should not be a COP, as it part_of embryo sac which is_a megagametophyte which is_a whole plant This was classified back when we were looser with putting things under COP. Need to propose an alternative classification.
• there are a number of parts of fruit such as the fruit septum (PO:0025268), fruit locule, fruit valve that should have dual parentage- e.g. fruit septum is_a septum (is_a col. organ part structure) and should also be is_a cardinal part of a multi-tissue plant structure.

Top levels of plant structure development stage branch

under construction

current structure:

At the POC Conf. Call 8-14-12, we had a discussion about whether or not it is necessary to mirror all the upper level terms from the PAE or just add the relevant parent categories needed for the classes such as "flower development" or "corolla development. Decided that it needed additional study and that for the mean time, we will develop the hierarchy with out them and compare the two approaches.

proposed structure without mirror of PEA branch:

primordium

RW: fixed errors in comment.

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)

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).

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)

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.

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

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, fruit, and inflorescence development stages

We currently have terms for:

• flower development stage (PO:0021004) five subclasses
• fruit development stage (PO:0001002) no subclasses
• inflorescence development stage (PO:0021004) - has two subclasses

The last two, in particular, are poorly developed (few specific subclasses)

It is far too easy to confuse these terms with:

• 4 flowering stage (PO:0007016)
• 5 fruit formation stage (PO:0007042)
• 3 inflorescence detectable stage (PO:0007047)

all of which are subclasses of sporophyte reproductive state (PO:00071300), meaning that they should only be used to describe the development state of a whole plant.

The first and easiest step to be taken would be to change the names of the whole plant development stages to make it clear that they apply to whole plants. For example, 4 flowering stage could be renamed flowering whole plant development stage. The definitions should probably be tweaked accordingly.

Flower development stage (PO:0021004) needs some work, but at least there is a good selection of terms for annotators to pick from.

For fruit development stage and Inflorescence development stage we need to develop at least some basic subclasses. For example, the plant phenotype pilot project needs terms for fruit development stages such as milk stage (as synonym for more general term) and mature or dry stage. These stages could (should?) parallel the stages for whole plants.

Flower development stage (PO:0021004) and subclasses

current def.: Stages of development of a flower defined by characteristic morphological, structural, histological or other visible features.

Proposed def.: A collective plant organ structure development stage (PO:new) that has as primary participant a flower (PO:0009046).

comment: (from original def.) Defined by characteristic morphological, structural, histological or other visible features. May have as parts the development stages of floral parts such as a gynoecium development stage (PO:0007606) or a corolla development stage (PO:0007604).

flower organ development stage

Should be an inferred class (like floral organ), and the subclasses should move to their proper parent. For example, gynoecium development stage and corolla development stage should be collective plant organ structure development stages and palea development stage should be a phyllome development stage. These classes should be part_of flower development stage, not is_a.

1 flower meristem visible stage (PO:0007601)

Current def.: Stage of flower development marked by the emergence of the floral meristem on the flank of the inflorescence meristem.

Needs to refer to apical meristem, not inflorescence meristem (same for the rest of them).

Growth forms

From Daniel Hiss: "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