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receptacle

(PO:0009064)

A receptacle can be part_of either a pedicel or a peduncle as stated in definition. Add relation part_of shoot axis, to be more specific.

proposed definition: A cardinal organ part (PO:0025001) that is the distal region of either a peduncle (PO:0009053) or a pedicel(PO:0009052) where the sepals (PO:0009031), tepals (PO:0009033), petals (PO:0009032), stamens (PO:0009029), and carpels (PO:0009030) are attached.

Question: Is a receptacle part of a flower? It was originally. It could stay part of shoot axis and also be part of flower.

PJ: Does this violate the part_of flower knowledge that flower parts are those parts that develop from floral meristem?

There is a relation that says flower develops_from flower meristem. Does the distal end of a pedicel or peduncle develop from that flower meristem? I think yes. The receptacle is developing at the same time as the other flower structures and is an integral part of the flower.

Talked to Dennis and Larry, and they agreed that the receptacle develops form the flower apical meristem. In fact, for much of development, the receptacle is the apical meristem, as the floral organ primordia are arising from it.

"Receptacle" can also be used for the base of an inflorescence (as in composites). We should rename PO:0009064 "flower receptacle", and create a new term for "inflorescence receptacle".

gynoecium

Current def. of gynoecium (PO:0009062): A collective phyllome structure composed of two or more carpels.

Comment: In some cases, a gynoecium may consist of only one carpel, in which case annotations should go on carpel (PO:0009030). The word pistil is used synonymously with gynoecium, but if a gynoecium consists of a single carpel, then pistil may be used synonymously with carpel. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).

New proposed definition, gynoecium: A collective phyllome structure (PO:0025023) composed of one or more carpels (PO:0009030).

Comment: A gynoecium is usually composed of two or more carpels, but may have only a single carpel as part. If annotating gene expression to a gynoecium with a single carpel, the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).

androecium

We should modify the definition of androecium correspondingly.

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 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, and use special terminology for when they are fused (such as corona and synather).

seed and parts of seed

A seed develops from an ovule, which is a plant organ, but no one really thinks of a seed as an organ. A seed is not really a collection of organs or a collection of anything else. It is a plant structure in which an endosperm and an embryo (usually, and may be other things) are located.

parts of seed: hilum (PO:0020063), hilum groove (PO:0004719); arilloid (PO:0019022); seed funicle (PO:0006332)(>stalk > COP); seed raphe (PO:0006331)

Hilum groove should be is_a plant anatomical space (or probably is_a canal). Maybe hilum can be is_a portion of tissue. Need to look into its histology.

Aril and ariloid could be multi-tissue structure or organism subdivision.

fruit

A fruit is a collective plant structure (now collective plant organ structure), because it develops from gynocium. However, if it develops from a single carpel, it develops from a single organ. It is kind of like a seed, in that it is not really considered an organ or made up of multiple organs.

Maybe this could be a subtype of whatever category we make up for seed.

background - CARO

How do CARO treat these?

From CARO2:

multi-cell-part structure: A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. -- example is neuron projection bundle. We don't really have a need for this term. I just put it here to show how they dealt with something very similar to our "collective organ part structure". We could have "multi-organ-part structure" as a synonym, but it's not necessary.

multicellular anatomical structure: Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by integument. -- This is the parent to the terms below. This is a very general term that could be used for a seed as well as for organs and other collective structures. Tissue is also a child of this term.

connected anatomical system: Multicellular (anatomical) structure that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity. -- Example is an integumentary system. We don't really have any terms like this in the PO.

organism subdivision: Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by integument. -- Example is appendage. Maybe this is the place ovary and other structures that cannot be specified more precisely because of their variable nature.

multi-tissue structure: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component. This is basically the same as PO plant organ.

New and revised collective terms

new general term, collective plant structures

This class needs to cover collective plant organ structure, collective organ part structure, and things like a seed and its parts.

What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo.

structures that contain other organisms

Is it time to introduce the located_in relation to the PO?

collective plant organ structure

Changed name, and slight change to clarify that the two organs must be separate, not one part of the other.

New proposed def.: A collective plant structure (PO:id) that is a proper part of a whole plant (PO:0000003) and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).

comment: A collective plant structure must have as parts at least two organs that do not have a part of relation between them, that is, one must be adjacent to the other, rather than one part of the other. The organs in a collective plant structure can be of the same type, such as a corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006) composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.

Modified comment for plant organ:

new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.

comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094).

Slight modification to cardinal organ part (add comment to see also COPS, add ids):

cardinal organ part (PO:0025001), proposed def.: A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.

comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.

cardinal part of collective plant structure

This is really just to cover the parts of a seed, because most other structures are a cardinal part of an organ or a collective organ part structure.

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]

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), 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

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.

PSDS term revisions

remaining terms needing name changes

Need to go through and add "stage" to the end of these terms:

PO:0007601 1 flower meristem visible

PO:0007056 1 pattern formation

PO:0007505 1 root primordium formation

PO:0007058 2 endoreduplication

PO:0007602 2 flower meristem notched

PO:0007527 2 root meristem formation

PO:0007061 2.00 main shoot only

PO:0007087 2.01 main shoot and axillary shoots visible at one node

PO:0007071 2.02 main shoot and axillary shoots visible at two nodes

PO:0007080 2.03 main shoot and axillary shoots visible at three nodes

PO:0007088 2.04 main shoot and axillary shoots visible at four nodes

PO:0007093 2.05 main shoot and axillary shoots visible at five nodes

PO:0007118 2.06 main shoot and axillary shoots visible at six nodes

PO:0007122 2.07 main shoot and axillary shoots visible at seven nodes

PO:0007077 2.08 main shoot and axillary shoots visible at eight nodes

PO:0007110 2.09 main shoot and axillary shoots visible at nine or more nodes

PO:0007059 3 branch formation

PO:0007525 3 establishment of tissue systems

PO:0001053 3 leaf fully expanded

PO:0007616 4 anthesis

PO:0007016 4 flowering

PO:0007135 4 growth directionality

PO:0001031 4 root elongation

PO:0007042 5 fruit formation

PO:0007617 5 post anthesis

PO:0007519 5 root hair formation

PO:0007075 5.02 20% of inflorescence emerged.

PO:0007102 5.04 40% of inflorescence emerged

PO:0007105 5.06 60% of inflorescence emerged

PO:0007107 5.08 80% of inflorescence emerged

PO:0007010 6 ripening

PO:0007121 6.01 10% of flowers open

PO:0007124 6.03 30% of flowers open

PO:0007125 6.04 40% of flowers open

PO:0007035 7-8 fruit formation and maturation

PO:0007126 7.02 fruit size 20%

PO:0007127 7.04 fruit size 40%

PO:0007128 7.06 fruit size 60%

PO:0007129 7.08 fruit size 80%

PO:0001005 A archesporial cells visible

PO:0007623 A megaspore mother cell enlarges

PO:0007503 A2.1 root intials differntiation of primary roots

PO:0007528 A2.2 root initials differentiation of lateral roots

PO:0007530 A2.3 founder cell derivatives of lateral root

PO:0007534 A2.4 root initials differentiation of crown roots

PO:0001018 B formation of primary parietal and sporogenous cells

PO:0007624 B meiosis of megaspore mother cell

PO:0007524 B1 primary root meristem formation

PO:0007539 B2 lateral root meristem formation

PO:0007514 B3 crown root meristem formation

PO:0001008 C callose wall formation in pollen mother cells

PO:0001025 C four anther lobes formed

PO:0007625 C tetrad of megaspores

PO:0007521 C3.1 metaxylem differentiation of root.

PO:0007537 C3.2 maturation of phloem elements in root.

PO:0007533 C3.3 maturation of protoxylem elements in root.

PO:0021002 calyx absolute size

PO:0021003 calyx relationship

PO:0007618 carpel primordium visible

PO:0001041 chalazal and micropylar domain establishment

PO:0004502 closure of carpel(s)

PO:0007518 crown root emergence

PO:0007504 crown root primordium formation

PO:0001026 D locules established

PO:0007626 D megaspore degeneration

PO:0007529 E emerged root elongation

PO:0001032 E tapetum degeneration initiated

PO:0007627 E two nucleate megagametophyte

PO:0007081 early rosette growth

PO:0001028 elongation zone formation

PO:0007523 establishment of initial cells

PO:0007628 F four nucleate megagametophyte

PO:0007531 F1 root hair initiation

PO:0007526 F2 root hair elongation

PO:0007026 FL.00 first flower(s) open

PO:0007034 FL.01 1/4 of flowers open

PO:0007053 FL.02 1/2 of flowers open

PO:0007052 FL.03 3/4 of flowers open

PO:0007024 FL.04 end of flowering

PO:0001099 formation of aleurone and starchy layers

PO:0001019 formation of leaf primordium

PO:0004500 formation of leaflet primordia

PO:0001021 formation of ligule primordium

PO:0001098 formation of starchy endosperm

PO:0001003 formation of the leaf founder cells

PO:0007036 FR.00 beginning of fruit ripening

PO:0007038 FR.04 fruit ripening complete

PO:0001057 fully expanded lemma

PO:0001079 fully expanded lodicule

PO:0001071 fully expanded palea

PO:0007612 fully expanded petal

PO:0001045 fully expanded sepal

PO:0001042 functional specialization of the endosperm

PO:0001035 G anther dehiscence

PO:0007629 G eight nucleate megagametophyte

PO:0004501 gynoecium differentiation and expansion

PO:0001036 H anther senescence

PO:0001020 hood-shaped primordium

PO:0007025 IE.00 inflorescence tip just visible above flag leaf sheath

PO:0007048 IE.01 1/4 of inflorescence emerged from flag leaf sheath

PO:0007008 IE.02 1/2 of inflorescence emerged from flag leaf sheath

PO:0007002 IE.03 3/4 of inflorescence emerged from flag leaf sheath

PO:0007023 IE.04 inflorescence fully emerged from flag leaf sheath

PO:0007076 late rosette growth

PO:0007517 lateral root emergence

PO:0007511 lateral root primordium formation

PO:0007133 leaf production

PO:0001055 lemma primordia visible

PO:0025337 life of whole plant

PO:0001072 lodicule primordia visible

PO:0007094 LP.01 one leaf visible

PO:0007098 LP.02 two leaves visible

PO:0007106 LP.03 three leaves visible

PO:0007115 LP.04 four leaves visible

PO:0007065 LP.05 five leaves visible

PO:0007123 LP.06 six leaves visible

PO:0007063 LP.07 seven leaves visible

PO:0007095 LP.08 eight leaves visible

PO:0007101 LP.09 nine leaves visible

PO:0007103 LP.10 ten leaves visible

PO:0007116 LP.11 eleven leaves visible

PO:0007064 LP.12 twelve leaves visible

PO:0007083 LP.13 thirteen leaves visible

PO:0007085 LP.14 fourteen leaves visible

PO:0007104 LP.15 fifteen leaves visible

PO:0007119 LP.16 sixteen leaves visible

PO:0007067 LP.17 seventeen leaves visible

PO:0007072 LP.18 eighteen leaves visible

PO:0007120 LP.19 nineteen leaves visible

PO:0007082 LP.20 twenty or more leaves whorls visible

PO:0001027 meristamtic zone formation

PO:0001000 meristem eloboration

PO:0007068 mid rosette growth

PO:0007060 obsolete growth and development terms

PO:0007532 obsolete plant growth and development terms

PO:0004504 ovule differentiation and expansion

PO:0007620 ovule primordium visible

PO:0001058 palea primordia visible

PO:0007608 petal primordium visible

PO:0028001 plant life cycle phase

PO:0007506 primary root primordium formation

PO:0001023 rapid elongation of leaf blade

PO:0001024 rapid elongation of leaf sheath

PO:0007501 root cap formation

PO:0007513 root cortex differentiation

PO:0007510 root emergence

PO:0007516 root epidermal differentiation

PO:0007536 root primordium visible

PO:0007509 root vascular cylinder differentiation

PO:0007113 rosette growth

PO:0007078 rosette growth complete

PO:0007079 SE.00 stem elongation begins

PO:0007091 SE.01 one node or internode visible

PO:0007117 SE.02 two nodes or internodes visible

PO:0007096 SE.03 three nodes or internodes visible

PO:0007092 SE.04 four nodes or internodes visible

PO:0007086 SE.05 five nodes or internodes visible

PO:0007062 SE.06 six nodes or internodes visible

PO:0007108 SE.07 seven nodes or internodes visible

PO:0007070 SE.08 eight nodes or internodes visible

PO:0007066 SE.09 nine nodes or internodes visible

PO:0007084 SE.10 ten nodes or internodes visible

PO:0007114 SE.11 eleven nodes or internodes visible

PO:0007111 SE.12 twelve nodes or internodes visible

PO:0007090 SE.13 thirteen nodes or internodes visible

PO:0007097 SE.14 fourteen nodes or internodes visible

PO:0007074 SE.15 fifteen nodes or internodes visible

PO:0007100 SE.16 sixteen or more nodes or internodes visible

PO:0007099 SE.97 flag leaf visible

PO:0007109 SE.99 maximum stem length reached

PO:0007607 sepal primordium visible

PO:0007610 sepals 100% of final size

PO:0007609 sepals 50% of final size

PO:0001380 sepals enclosing flower bud

PO:0001378 sepals enclosing meristem

PO:0001030 specialization zone formation

PO:0007613 stamen primordium visible

PO:0007089 stem elongation

PO:0004503 stigma cell differentiation

PO:0001095 true leaf formation

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

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