Items In Progress

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Unfinished items from older agendas

lobe and tooth

Post-poned until next week's discussion. Details moved to Items for future meetings

Last week 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.

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

part_of organ margin

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

part_of leaf phyllome margin

proposed definition, leaf lamina lobe: A phyllome lobe that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)

part_of leaf lamina margin

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, phyllom 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?)

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.

Primordia

These issues came up while we were working on new term requests for Agrinomics.

primordium (PO:0025127): A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]

Comment: The primordium is the first distinct form in the development of a plant structure.

leaf primordium: A phyllome primordium that will develop into a leaf. [source: POC:Curators]

Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).

I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.

"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."

General question: Do these tissues only occur in the primordium, or continue on after it becomes a young leaf? When does it stop being a primordium? If these tissues are all part of LP, then presumably the LP ends when cell stop dividing. I think usually the term primordium is used for the earliest stage of an organ's development, not all the way up until cell division ceases. Maybe better to say they develop from LP and are part_of leaf during PO:0001052 leaf expansion stage.

We felt primordium should probably be an organ. All primordia have at least two types of tissue - protoderm and ground meristem(?).

Primordium ends and leaf begins with the formation of the different meristems (adaxial, plate) that contribute to the final form of a leaf.

Problem with having different types of primordia as organs means they will all have dual parentage (is_a primordium and is_a whatever type of organ. We were trying to get rid of that when we made it is_a tissue.

promeristem as synonym of AM, not RAM

User requests open on Source Forge; PSDS

coleoptile emergence

This was discussed at the NYBG Meeting, on Sunday_Sept_11th,_2011

We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed. (rather than above ground)

This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.

At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.

Comment: This terms is used only for seed plants.

proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.

Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???

Comment: This terms is used only for seed plants.

proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???

Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.

current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence from growth medium development stage (PO:0007049): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

proposed: cotyledon emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.

current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence from growth medium development stage (PO:0007054): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.

proposed: epicotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.

current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence from growth medium development stage (PO:0007043): A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

proposed: hypocotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.

Could also add terms for feeder emergence for some gymnosperms.

For all of the above terms, need to check existing synonyms and move or copy them as needed.

tuber growth and development stages

This item has been open on SF since 6/2009

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 PGDSO

l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926

User requests open on Source Forge: PAO

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

areole

Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).

Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).

is_a axillary bud

ref.: Bell and Bryan, Plant Form

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.

Vascular tissues and cell types

THIS PART IS STILL UNDER CONSTRUCTION

These terms will need to be fixed before the Wood Ontology meeting in February.

vascular tissue types

For vascular plants, we have the class:

portion of vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]

Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.

part_of vascular bundle (which is part_of vascular system)

This is okay, but suggest that we change definition to include xylem or phloem, and it may not always be part_of vascular bundle.

Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve elements.

Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissues or cells, such as parenchyma or fibers.

part_of vascular system (should add vascular system participates_in sporophytic phase)

vascular bundle (PO:0005020) current def.: A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]

This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.

proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.

Comment: Usually contains both xylem and phloem. May also contain other types of cells or tissue such as fibers, vascular cambium, or portions of ground tissue.

part_of vascular system

add vein as exact synonym -- can be in any organ

primary and secondary vascular tissue

primary vascular tissue: A portion of vascular tissue that develops from a procambium. (ref: Esau)

comment: Forms as part of primary growth (GO:xxxx).

secondary vascular tissue: A portion of vascular tissue that develops from a vascular cambium. (ref: Esau)

comment: Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system and ray system.

If we set both of these up as a cross products, then primary and secondary xylem and phloem will be inferred children.

phloem

phloem (PO:0005417) current def.: A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]

proposed definition: A portion of vascular tissue that has as parts sieve elements.

Comment: Functions in the conduction of organic substances in vascular plants.

Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.

metaphloem (PO:0006076) current def.: Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

proposed definition: A portion of primary phloem that differentiates after the protophloem.

Comment: Differentiates before the secondary phloem, if any is formed.

protophloem (PO:0006077) current def.: The first-formed elements of the primary phloem.

proposed definition: A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.

primary phloem (PO:0006075) current def.: A portion of phloem tissue of the primary plant body.

proposed definition: A portion of phloem tissue that develops from the procambium.

Comment: Primary phloem develops as part of GO:xxxx primary growth. (see below)

develops_from PO:0025275 procambium

secondary phloem (PO:0005043) current def.: A portion of phloem tissue formed by the activity of the vascular cambium.

proposed definition: A portion of phloem tissue that develops from the vascular cambium.

Comment: Secondary phloem develops as part of GO:0080117 secondary growth.

develops_from PO:0005598 vascular cambium

xylem

xylem (PO:0005352) current def.: A portion of vascular tissue composed of xylem elements.

comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.

proposed definition: A portion of vascular tissue that has as parts tracheary elements.

comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.

primary xylem (PO:0005849) current def.: A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194]

Comment: In stem or root it is differentiated behind the apical meristem.

proposed definition: A portion of xylem tissue that differentiates from the procambium.

Comment: Primary xylem develops as part of GO:xxxx primary growth.

develops_from PO:0025275 procambium

protoxylem (PO:0000272) current def.: A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208]

proposed definition: A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.

metaxylem (PO:0000372) current def.: A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208]

proposed definition: A portion of primary xylem that differentiates after the protoxylem.

Comment: Differentiates before the secondary xylem, if any is formed.

secondary xylem (PO:0005848) current def.: A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]

Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.

Existing definition is okay.

New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial and ray systems. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed of secondary xylem.

develops_from PO:0005598 vascular cambium

Note: exarch, endarch, mesarch are descriptors for different types of xylem development.

tracheid bar (PO:0019026) current def.: A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]

proposed definition: A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.

Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]

part_of seed; adjacent_to hilum

leaf vein, midrib, costa

• leaf vein (PO:0020138), current def: A strand of vascular tissue in the leaf blade.

is_a portion of vascular tissue; part_of leaf vascular system

proposed definition, leaf vein (PO:0020138): A vascular bundle that is part of a leaf lamina in a vascular leaf.

part_of leaf vascular system, part_of leaf lamina

synonym: leaf vascular bundle

Suggest new term primary leaf vein: A leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.

Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).

• midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]

Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.

proposed definition: A primary leaf vein that is the central vein of a vascular leaf.

Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf.

broad synonyms: mid rib, midrib, mid-rib, vascular leaf midvein

related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128

We already have terms for secondary, tertiary, quaternary, and higher order veins.

Primary and secondary growth, lateral meristems, etc.

proposed terms for GO

primary growth (new term):

proposed definition: Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)

comment: Has its inception in the apical meristems and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.

is_a growth (GO:0040007)

secondary or lateral growth

GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290

Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by Rudall et al. in Botanical Review.

Perhaps GO should have a general term for lateral growth (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.

lateral growth (GO:new term): Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).

Comment: Includes thickening of plant axes due to the activity of a cambium (secondary growth, found in most gymnosperms and dicotyledons), a primary thickening meristem (found in many monocotyledons, some ferns and some cycads), or secondary thickening meristem (in some monocotyledons).

proposed new def., secondary growth (GO:0080117): Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)

Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium (phellogen). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.

Add synonym "cambial secondary growth", which is makes the meaning clearer.

secondary thickening (GO:new term): Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:xxxx).

comment: Occurs shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.

References: Fahn 1990, ISBN:0080374903, Rudall 1991, JSTOR:4354165

primary thickening (GO:new term): Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)

comment: Occurs in shoot axes and rarely in roots in many monocotyledons.

Ref: JSTOR:4354165, Rudall 1991, and Esau ISBN:0471245208

diffuse secondary thickening (GO:new term): Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fibers of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.

comment: Occurs in the stems of some Arecaceae (palms).

Ref.: Fahn 1990, ISBN:0080374903

PO terms for lateral meristems

The PO has a general term for lateral meristem, of which cambium is a subtype:

lateral meristem (PO:0020145)

current def.: A meristem containing cells along the stem or root that first differentiate and function as members of a mature tissue system but then again take up meristematic activity.

proposed def.: A meristem located parallel to the circumference of a plant organ.

comment: Participates in lateral growth (GO:xxxx) of a plant organ, primarily shoot axes and roots. Contrast with apical meristem (PO:0020144).

root lateral meristem (PO:0006308)

current def.: Meristem of the root located parallel to the sides of the axis.

comment: Generally causes root thickening. Not to be confused with lateral root meristem, which is the meristem of the lateral root.

This is just a cambium in the root, which also has vascular cambium and phellogen.

proposed new name and def.: root cambium: A cambium that is part of a root.

This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.

If we are going to have this term, maybe we should have root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium?

cambium (PO:0005597)

current def.: A lateral meristem, the cells of which divide mostly periclinally. [source: ISBN:0080374913]

proposed def.: A lateral meristem that has a part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files. (Ref.: Esau)

comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).

vascular cambium (PO:0005598)

current def.: A lateral meristem, the cells of which give rise to secondary xylem and phloem, leading to an increase in girth.

Current definition is okay, but needs minor changes.

proposed def.: A cambium that gives rise to secondary xylem and secondary phloem.

comment: Vascular cambium is located between the secondary xylem and secondary phloem and gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis.

cork cambium/phellogen (PO:0005599)

current def.: Lateral meristem which produces the phellem (cork) and the phelloderm.

proposed def.: A cambium that is part of a periderm and produces phellem (cork) and phelloderm.

comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.

primary thickening meristem (PO:0005039)

current def.: A meristem that develops from a peripheral zone of a shoot apical meristem and is responsible for the primary increase in thickness of a shoot axis.

comment: May appear as a distinct mantle like zone. Often found in monocotyledons.

Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.

proposed def.: A lateral meristem that has a parts multiple layers of cells located near the shoot apical meristem.

comment: Contributes to primary thickening of the stem, adventitious root formation, and formation of linkages between the stem, leaf, and root vasculature. Contiguous with the shoot apical meristem in some species, but not all. Produces more or less distinct vascular bundles surrounded by ground tissue, as opposed to the more or less continuous xylem and phloem produced by a vascular cambium. A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.

secondary thickening meristem (new term)

proposed def.: A lateral meristem has a parts multiple layers of cells in a shoot axis...

comment: Contributes mainly to formation of the body of a stem, but may also produce adventitious roots. May be continuous or discontinuous with the primary thickening meristem. Found in some monocot species of the Liliales and Asperigales.

Other types of lateral meristems

PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel merristem (PO:0009107), plus their subtypes.

Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches generall develop from apical meristems, not a lateral meristem.

There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.

inflorescence lateral meristem (PO:0009105)

current def.: The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.

This should be called inflorescence branch meristem, and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.

ear lateral meristem (PO:0009110)

current def.: The meristem that gives rise to the lateral structures of a maize ear.

This should be called ear inflorescence branch meristem, and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).

proposed def.: An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.

conductive and related cell types

Current parent: axial cell

Existing structure:

axial cell (PO:0000081)

>sieve tube member (PO:0000289, alt: PO:0000286)

>phloem fiber (PO:0004519)

>xylem element (PO:0000273)

>>tracheary element (PO:0000273)

>>>tracheid (PO:0000301)

>>>vessel member (PO:0002003)

>>xylem fiber (PO:0000274)

>>>fiber tracheid (PO:0000355)

>>>libriform fiber (PO:0004520)

>>>septate fiber (PO:0004521)

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]

Comment: These cells make up the axial system, also known as vertical or longitudinal system.

The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.

See Items for future meetings#other wood terms, below.

New proposed hierarchy (children of plant cell):

plant cell

>sieve element (new term)

>>sieve tube member (syn.: sieve tube element)

>>sieve cell (new term)

>tracheary element

>>tracheid

>>vessel member

>ground tissue cell (PO:0025030)

>>sclerenchyma cell (PO:0000077)

>>>sclerid (new term)

>>>fiber cell (new term)

>>>>phloem fiber cell

>>>>xylem fiber cell

>>>>other kinds of fiber cells?

New definitions - sieve elements

Definitions from Esau's Anatomy of Seed Plants

sieve element (new term)

From Esau (glossary): The cell in the phloem tissue concerned mainly with longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.

Also from Esau (in text): Their principal morphological characteristics are sieve areas (modified pits) in their walls and the absence of nuclei in mature protoplasts.

proposed def.: A plant cell that is part of a portion of phloem tissue, has sieve areas (modified pits) in its walls, and lacks a nucleus in its mature protoplast.

Comment: Sieve cells function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.

part_of phloem, participates_in sporophyte stage

sieve cell (new term)

proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.

Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas.

sieve tube member (PO:0000289)

current def.: One of the series of cells that make up a sieve tube; it shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores).

comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.

proposed def.: A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.

Comment: Sieve elements have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.

syn.: sieve tube element, sieve tube segment

part_of sieve tube (new term)

See below for companion cells and other parenchyma cells found in vascular tissue.

New term for sieve tube

sieve tube, proposed definition: A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.

New terms for GO

These subcellular components have been requested from GO.

sieve area: A cell wall part that is a pit-like area in a plant-type cell wall of a sieve element and has as parts pores lined with callose and occupied by strands of protoplasmic material that interconnect the protoplasts of contiguous sieve elements.

is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505); part_of sieve element (PO:xxxx) - may have to go in comment

sieve plate: A cell wall part that is the part of a wall of a sieve tube member that bears one or more highly specialized sieve areas.

comment: Typical of angiosperms.

is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505), has_part sieve area (GO:xxxx); part_of sieve tube member (PO:xxxx).

Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.

compound sieve plate: A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.

comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.

is_a sieve plate

simple sieve plate: A sieve plate that has as part a single specialized sieve area.

comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.

New definitions - tracheary elements

xylem element (PO:0000273): A cell making up xylem tissue.

Currently, this is parent of tracheary element and xylem fiber. I suggest we obsolete it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber.

tracheary element (PO:0000290)

current def.: General term for any water conducting cell, tracheid or vessel member.

Currently is part_of primary xylem and part_of secondary xylem.

proposed def.: A plant cell that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.

comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells by the presence of bordered pits, although there are intermediate forms called fiber tracheids.

participates_in sporophyte stage, part_of xylem, disjoint from hydroid

tracheid (PO:0000301)

current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.

proposed def.: A tracheary element that has no perforations.

comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members it has perforations organized into perforation plates.

vessel member (PO:0002003)

current def.: One of the cellular components of a vessel, a dead cell with the wall between adjacent members being variously perforated and the walls that persist variously thickened.

proposed def.: A trachary element that is part of a vessel and has as parts perforation plates.

Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (GO:xxxx). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.

syn.: vessel element, vessel segment

part_of vessel (new term)

vessel (new term)

proposed def.: A portion of vascular tissue that has as parts a tube-like series of vessel members, the common walls of which have perforations.

perforation plate (for GO)

proposed def.: A cell wall part that is the part of a wall of a vessel member that bears one or more openings (perforations).

comment: May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.

New definitions - ground tissue cells

sclerenchyma cell (PO:0000077)

current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.

proposed def.: A ground tissue cell with thickened secondary cell walls that are often lignified.

comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from xylem tissue or sclerified parenchyma cells.

Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.

sclerid (new term)

proposed def.: A sclerenchyma cell that has thick, lignified secondary walls with many pits.

comment: Usually not very elongated.

parenchyma cells in vascular tissue

companion cell (PO:0000071)

current definition: A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.

proposed definition: A parenchyma cell that is adjacent to a sieve-tube member and arises from the same mother cell as the sieve-tube member.

comment: Found in angiosperms. Compare to albuminous cells (PO:xxxx), which are found in gymnosperms.

Currently part_of primary phloem and part_of secondary phloem, which can't be true. Should change to part_of phloem.

Suggest that we add relation companion cell adjacent_to sieve tube element.

albuminous cell (new term)

proposed def.: A parenchyma cell that is morphologically and physiologically associated with a sieve cell but does is not derived from the same initial cell as the sieve cell.

comment: May be found in the rays and sometimes the axial system of gymnosperms. Compare to companion cells, which are found in angiosperms.

is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.

Should we have a term for phloem parenchyma cell? Could be parent of companion cell and albuminous cell.

fiber cells

fiber cell (new term)

proposed def.: An elongated, tapering schlerenchyma cell with a more or less thick secondary cell wall.

comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from xylem cells.

phloem fiber cell (PO:0004519) (was called phloem fiber)

current def.: A fiber in phloem.

proposed def.: A fiber cell that is part of a portion of phloem tissue.

xylem fiber cell (PO:0000274) (was called xylem fiber)

current def.: A fiber in xylem.

proposed def.: A fiber cell that is part of a portion of xylem tissue.

comment:

libriform fiber (PO:0004520)

current def.: A xylem fiber commonly with thick walls and simple pits.

proposed def.: A xylem fiber cell with simple pits.

Comment: Libriform fibers have unbordered pits while fiber tracheids have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fibers and fiber tracheids are present, the libriform fibers usually have thicker walls. Libriform fibers have a slit-like aperature toward the cell lumen, but no pit cavity.

fiber tracheid (PO:0000355)

current def.: A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.

Should this be is_a xylem fiber or is_a tracheid? Esau's definition says it is a tracheid, but her treatment it the book is as a fiber.

proposed definition: A xylem fiber cell with bordered pits with pit cavities.

comment: If both libriform fibers and fiber tracheids are present, the libriform fibers usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessels or tracheids of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.

septate fiber (PO:0004521)

current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.

Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.

proposed definition, septate fiber tracheid: A fiber tracheid that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate libriform fiber: A libriform fiber that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate phloem fiber: A phloem fiber cell that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

other kinds of fiber cells?

gelatinous fiber: A xylem fiber cell in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.

comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.

ref: Fahn

synonym: mucilaginous fiber

extraxylary fiber? - a fiber cell outside the xylem. Would include phloem fibers, fibers as idioblasts, and fibers in ground tissue.

other wood terms

Wood is a synonym for secondary xylem (PO:0005848) -- see definition above.

axial system: A portion of plant tissue that has as parts cells derived from the fusiform cambial initials and oriented with their longest diameter parallel to a root or shoot axis.

comment: Includes portions of secondary xylem tissue and axial wood parenchyma tissue.

synonyms: vertical system, longitudinal system

ray system: A portion of parenchyma tissue that has as parts all of the ray wood parenchyma in a plant structure.

comment: May refer to the ray system of a shoot axis, a root, or an entire plant.

synonyms: radial system, horizontal system

wood parenchyma (PO:0004532):

Current def.: Parenchymatous tissue occurring in the wood.

is_a secondary xylem. Should be is_a parenchyma.

Proposed def.: A portion of parenchyma tissue that is part of a portion of secondary xylem.

wood parenchyma cell (PO:0004525):

Current def.: Parenchyma cell occurring within secondary xylem.

Proposed def.:

axial wood parenchyma (PO:0004533):

Current def.: Parenchyma tissue in the axial system of secondary xylem.

axial wood parenchyma cell ; PO:0004526 Parenchyma cell in the axial system of secondary xylem. plant anatomy

procumbent wood ray parenchyma cell ; PO:0004529 Ray cell within secondary xylem having its longest axis in radial direction.

ray wood parenchyma (PO:0004534):

Current def.: Radially oriented parenchyma tissue in secondary xylem.

Proposed def.: A portion of parenchyma tissue that develops from ray initials and extends radially in the secondary xylem and phloem of a plant axis.

comment: Occurs in bands or rays of variable width and height. The term ray system is used to describe all of the rays in a plant structure.

part_of ray system

ray wood parenchyma cell (PO:0004527):

Current def.: Parenchyma cell of a ray in secondary xylem.

Proposed def.: A parenchyma cell that is part of a portion of ray wood parenchyma.

upright wood ray parenchyma cell ; PO:0004528 Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.

sapwood (PO:0004513):

Current def.: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.

early wood ; PO:0004515 The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.

heartwood ; PO:0004512 The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.

late wood ; PO:0004516 The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.

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.

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