POC Conf. Call 4-28-11

POC meeting, Webex Conference Call; Date: Thursday April 28th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Justin Elser (OSU)?, Pankaj Jaiswal (OSU),

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_4-26-11? There were no changes, additions or deletions.

Items arising from previous meetings:

plant embryo (PO:0009009)

Added child new terms:

* zygotic plant embryo (PO:0025303):def'n: A plant embryo that forms as a result of the fusion of gametes. is_a plant embryo

*somatic plant embryo (PO: 0025302): A plant embryo that arises from previously differentiated somatic cells, rather than from fused haploid gametes, i.e., the zygote.

Comment: Somatic plant embryo may arise where embryos normally would not arise, i.e. on the edges of leaves on Kalanchoe or ferns,

We will use the term 'apomictic plant embryo' as an exact synonym (rather than renaming).

Children of cultured plant embryo:

* cultured zygote-derived plant embryo (PO:0025304): def'n: A zygotic plant embryo that is grown or maintained in culture. exact synonym: cultured zygotic embryo, is_a zygotic plant embryo, and is_a cultured plant embryo

*microspore-derived cultured plant embryo (PO:0025305):def'n: A cultured plant embryo that develops from isolated microspores.

is_a cultured somatic plant embryo, exact synonym: microspore-derived haploid embryo

Terms and definitions were accepted

Renamed:

*cultured somatic plant embryo (PO:0000011) def'n: A somatic plant embryo grown or maintained in vitro.

is_a somatic plant embryo and also a cultured plant embryo

*nucellar plant embryo (formerly adventitious embryo)(PO:0004537): A somatic plant embryo derived directly from nucellus cells.

Comment: Also known as apomictic plant embryo, common in Citrus. synonyms broad; adventitious embryo, apomictic plant embryo

We will not use the term 'apomictic plant embryo' as an broad synonym here. Revised comment: Commonly found in Citrus

The Dandelion example would go to somatic plant embryo.

apical cell

Moss Ontology has requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.

Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.

The term apical cell (PO:0004000) was obsoleted and replaced by embryonic apical cell (PO:0025284) for clarity. A new term apical cell (PO:0030007) is the general class for all apical cell types.

Definition of apical cell from Esau: The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.

Definition of apical cell from Crum: A single cell at the tip of a stem, leaf, leaf or other structure that divides repeatedly to form new cells; also known as an apical intial.

Is apical cell more consistent with meristematic cell (A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall) or with initial cell (A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body)? Probably meristematic cell, because all of the daughter cells of an apical cell may remain meristematic.

Proposed def. of apical cell (PO:0030007): A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex, or thallus apex.

Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo or later.

-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.

There was some discussion last week of whether or not apical cell should be is_a initial cell. It is important that the definition make it clear that this is not just any meristematic cell that is part of a shoot apex, but that it is one specific cell. Should look at papers for gene expression in these cells and compare to expression in SAMs or RAMs of seed plants.

See: http://www.anbg.gov.au/bryophyte/case-studies/apical-cells.html

There was an extensive discussion, continuing from the one last week about whether we should keep the term 'apical cell' to refer to the very tip or apical cell in an angiosperm leaf or other structure. The problem of adding a generic term for an apical cell is that it would cause confusion. Additionally is there really a single cell at the tip of a vascular leaf? For cells at the leaf apex (PO:0020137) and leaf tip (PO:0025142), we can use the existing PO terms. We decided to go with the proposed changes below and perhaps reconsider the issue of general term 'apical cell' in the future.

Proposed rename: meristematic apical cell (PO:0030007):

Revised new def'n: A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex or thallus apex, in a plant structure (organ?) where apical growth occurs.

RW: Better to say plant structure, to include apical cells on embryo and protonema, which are not organs.

is_a meristematic cell, sibling to initial cell

In addition, to ensure clarity, we should append the names of the child terms with 'meristematic' in their names. Except for embryonic apical cell

We could use always_in and never_in taxon relations to help clarify which taxa these are from

New terms and definitions for apical cells

Apical cells are classified two ways: by structure and by gametophyte/sporophyte. Structural relations are asserted as is_a relations. The relations to gametophyte or sporophyte are inferred by the intersection_of terms.

At least week's meeting the definitions for the descendents of apical cell (listed below) were approved, pending approval of final definition of apical cell. See POC_Conf._Call_4-26-11#apical_cell for more details.

gametophytic apical cell (PO:0030014)

sporophytic apical cell (PO:0030015)

thallus apical cell (PO:0030025)

root apical cell (PO:0030008)

shoot apical cell (PO:0030009)

gametophore apical cell (PO:0030019)

leaf apical cell (PO:0030011)

non-vascular leaf apical cell (PO:0030013)

vascular leaf apical cell (PO:0030012)

shoot axis apical cell (PO:0030010)

gametophore axis apical cell (PO:0030023)

vascular shoot axis apical cell (PO:0030024)

seta apical cell (PO:0030016)

embryonic apical cell (PO:0025284, replaces PO:0004000)

Also need to add a term for protonema meristematic apical cell.

As stated above, all these child terms (embryonic apical cell) will be amended to with 'meristematic' in their names.

New terms for Physcomitrella and related taxa (continued)

Plant organs:

caulid/cauloid

- This is the term used for the gametophore stem or axis.

Suggest using gametophore axis (PO:0030020) as primary name, cauloid as exact synonym.

Proposed def'n: A shoot axis that is part of a gametophore.

Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.

intersection_of: is_a plant axis, intersection_of: part_of gametophore

Add caulome as synonym of shoot axis

-Also suggest adding terms for gametophore stem and gametophore branch.

gametophore stem (PO:0030022): A stem that is part of a gametophore.

is_a stem, part_of gametophore Add synonyms caulid stem and cauloid stem

gametophore branch (PO:0030021): A branch that is part of a gametophore.

is_a branch, part_of gametophore Add synonyms caulid branch and cauloid branch

-If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or branch).

Accepted

perigonial bract (PO:0030028)

- The specialized phyllids surrounding the antheridia.

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.

Proposed def'n: A bract that subtends an antheridium.

part_of gametophore

Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.

Accepted

In definition of bract (PO:0009055), "usually different from foliage leaves" should just say leaves, and go in comment.

foot

Moss Ontology definition: The base of the sporophytes in mosses

Proposed name and def.: sporophyte foot (PO:0030029): A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore. (ref: Schofeld)

Comment: Found in bryophytes and some pteridophytes. In mosses, the foot is located below the seta. In ferns, the foot is formed from the upper hypobasal quandrant of the embryo. The sporophyte foot serves for both attachment and absorption. The outer portion of the foot is composed of absorptive transfer cells. (ref: Crum)

participates_in sporophytic phase, has_part transfer cell

Accepted

Additional organ related moss terms:

These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we should add them now.

perichaetal bract (PO:0030030)

Proposed def.: A bract that subtends an archegonium. part_of gametophore

Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.

Accepted

gametophytic perianth (PO:0030031)

Proposed def.: A collective phyllome structure that consists of two or more of the most distal perichaetal bracts on a gametophore axis that surround a capsule.

-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)

Comment: The perichaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

Accepted

seta (PO:0030032)

-The stalk of a moss sporophyte.

Proposed def.: A plant axis that holds up a spore capsule. participates_in sporophytic phase

Comment: Found in some bryophytes, especially mosses.

Accepted

antheridiophore and archegoniophore

These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)

Proposed definitions:

antheridiophore (PO:0030033): A plant axis that bears two or more antheridia.

participates_in gametophytic phase

Comment: Antheridia are borne on a disk-shaped archegonial head. Found in Marchantiales.

archegoniophore (PO:0030034): A plant axis that bears two or more archegonia.

participates_in gametophytic phase

Comment: Archegonia are borne on an umbrella-shaped archegonial head. Found in Marchantiales.

Modify definitions slightly:

antheridiophore (PO:0030033): A plant axis that bears two or more antheridia on an antheridial head.

Comment: Found in Marchantiales.

archegoniophore (PO:0030034): A plant axis that bears two or more archegonia on an archegonial head.

Comment: Found in Marchantiales.

Add terms for antheridial head and archegonial head. (cardinal organ parts)

Will also add terms for antheridium stalk (PO:0030035) and archegonium stalk (PO:0030036):

A stalk that is the basal part of an antheridium/archegonium. part_of antheridium or archegonium.

Comment: Raises the antheridium/venter above the rest of the gametophyte.

Accepted

Cardinal organ parts

Terms requested by MO:

• calyptra

Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.

We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named perianth calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.

Proposed name and def.: spore capsule calyptra (PO:0030037): A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.

Comment: Found in bryophytes and pteridophytes. The calyptra is a membranous or hairy cap or hood composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.

participates_in gametophytic phase, develops_from archegonium

subsets for bryophytes, pteridophytes

Accepted

• venter (PO:0030038)

This term was not suggested by Moss Ontology, but we should add it.

proposed def.: A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.

part_of archegonium

subsets for bryophytes, pteridophytes, gymnosperms

Accepted

• archegonium neck(PO:0030039)

This term was not suggested by Moss Ontology, but we should add it.

proposed def.: A cardinal organ part that is the elongated apical part of an archegonium.

Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

part_of archegonium

(can also add term for neck canal cell when we deal with cells)

subsets for bryophytes, pteridophytes, gymnosperms

Accepted

• base

Proposed name and def.: sporangium base (PO:0030040): A cardinal organ part that is the basal part of a sporangium.

Comment: Term used in mosses and other bryophytes and some pteridophytes. The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)

part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis (Crum)

subsets for bryophytes, pteridophytes

In comment, say sporangium theca instead of just theca.

• theca

Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. We should call that anther theca and call this term sporangium theca:.

Proposed name and def.: sporangium theca (PO:0030041): A cardinal organ part that is the main body of a sporangium and has spores located in it.

Comment: Term used for bryophytes and pteridophytes.

part_of sporangium

subsets for bryophytes, pteridophytes

Accepted

• peristome (PO:0030042)

Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

proposed definition: A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.

Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.

part_of sporangium

subsets for bryophytes

PJ brought the following paper to our attention: 'ENIGMATIC PERISTOME'. This is not a special type of peristome, but a case of where the peristome is puzzling to the researchers. :-)

That publication mentions inner peristomal layer (IPL) and primary peristomal layer (PPL). Can investigate whether or not we should add those terms.

Revised definition: A single or double circle of peristome teeth inside a sporangium mouth.

Accepted

• peristome tooth (PO:0030043)

Not requested by Moss Ontology, but should add it.

Proposed def: A cardinal organ part that is a single lobe or tooth of a peristome.

Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.

part_of peristome

subsets for bryophytes

• Add term for peristome cell? Are they dead at maturity? What kind of cells are they?

Revised definition: A cardinal organ part that is a single lobe of a peristome.

Add to comment: Generally triangular.

Accepted

• lid/operculum

Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.

We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.

Proposed name and def.: spore capsule operculum (PO:0030044): A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.

Comment: Found in mosses. May remain partly attached to the rest of the capsule.

Synonym: sporangium lid

part_of sporangium

subsets for bryophytes

Accepted

Also add these terms for angiosperms:

fruit operculum (PO:0025298): A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence.

Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.

part_of fruit; disjoint_from spore capsule operculum

Accepted

perianth calyptra (PO:0025299): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary.

Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. May separate from the plant at maturity, exposing the capsular fruit and fruit operculum. Sometimes erroneously referred to as part of a fruit.

Rename calytpra perianth?

Remove "May separate from the plant at maturity, exposing the capsular fruit and fruit operculum" because it is confusing. May come off before the fruit matures and expose the stamens rather than the fruit.

Add floral calyptra and floral operculum as exact synonyms?

Accepted

Other related terms for mosses, not from Moss Ontology

• spore capsule mouth (PO:0030017)

Proposed definition: A plant anatomical space that is the opening on the apical end of a spore capsule.

Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.

part_of sporangium

subsets for bryophytes

PJ asked if the mouth was always apical on the capsule. RW will check that. Some capsule (e.g., in hornworts) split down the side, rather than with via an operculum, but then the term mouth is not used. Could add comment to that effect.

Accepted

• epiphragm (PO:0030054)

Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."

From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."

Proposed definition: A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule columella and attached to the ends of the peristome teeth that covers a spore capsule mouth.

Comment: Present in some moss species of the family Polytrichaceae.

Synonym: tympanum, epiphram

subsets for bryophytes , part_of sporangium

Accepted

• pseudopodium (PO:0030055)

From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."

From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."

Proposed definition: A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.

Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.

participates_in gametophytic phase

subsets for bryophytes

Revised definition: A gametophore axis that is a leafless extension of a gametophore stem on which a sporophyte is borne.

Need to check if it can also occur on a branch.

Accepted

Sporangium

We currently have the class sporangium (PO:0025094), which is a cardinal organ part.

Current def: A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]

Comment: May be multicellular or unicellular. In bryophytes, particularly in mosses, a sporangium is referred to as a capsule

In bryophytes, the sporangium is a plant organ. In seed plants, it is a cardinal organ part (part of a sporophyll). In ferns, it grows on the surface of a leaf and in other pteridophytes is grows on the surface of a sporophyll. It is legitimate to say that in seed plants, the sporangium is a reduced organ that is located in another organ.

It is not really hollow. It is full of sporocytes or spores.

Proposed definition: A plant organ in which spores are produced.

Comment: In bryophytes, particularly in mosses, a sporangium is referred to as a capsule. In seed plants, a sporangium is located in a sporophyll. In pteridophytes, a sporangium is located on the surface of a sporophyll or fertile leaf or borne on a sporangiophore. May be unicellular in some algae.

We also have:

megasporangium (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]

microsporangium (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]

nucellus (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]

Comment: In seed plants, the megaspores and megagametophyte are retained within the nucellus.

pollen sac (PO:0025277): A microsporangium that is part of a sporophyll where the pollen grains developed and are contained after they develop. [source: POC:curators]

Comment: A pollen sac is a microsporangium in seed plants. In angiosperms, a single, unfused pollen sac may contain an anther locule or several pollen sacs may fuse so they contain a single anther locule.

Proposed changes:

Definitions of mega- and microsporangium are fine.

The only differences below are substituting located in for other words.

Proposed def. nucellus: A megasporangium in a seed plant, composed of fleshy subepidermal tissue that is located in an ovule and surrounding a megasporocyte.

Proposed def. pollen sac: A microsporangium that is located in a sporophyll and where the pollen grains developed and are located after they develop. [source: POC:curators]

(comments stay the same)

We could continue to use the more general part_of relation for located_in, if we don't want to add a new relation.

The above changes were accepted.

Plant Cells

Terms requested by Moss Ontology:

archesporial cell

We have the terms:

female archesporial cell (PO:0006015): In the majority of flowering plants including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]

male archesporial cell (PO:0006014): It undergoes periclinal divisions, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]

Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.

Proposed definitions:

archesporial cell (PO:0030056) A plant cell that divides to gives rise to a sporocyte and is part of a sporangium.

Comment: May also give rise to sterile cells such as elators (in liverworts) or tapetal cells. In most species outside seed plants, multiple archesporial cells are part of an archesporium or sporogenous tissue.

synonym: sporogenous cell

female archesporial cell (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.

Comment: Found in heterosporous ferns and seed plants. May also give rise to sterile cells. In the majority of flowering plants, including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]

Made female archesporial cell part_of megasporangium, instead of part_of ovule primordium.

Made megasporocyte part_of megasporangium, instead of part_of nucellus.

male archesporial cell (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.

Comment: Found in heterosporous ferns and seed plants. May also give rise to sterile cells. In seed plants, a male archesporial cell undergoes periclinal division, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: PMID:10465788]

Made male archesporial cell part_of microsporangium, instead of part_of anther primordium.

Microsporocyte was already part_of microsporangium.

Definitions of male and female archesporial cell should say "An archesporial cell..."

Maybe we should remove the abbreviations from the comment? Check if they are in the PO.

Accepted

alar cell (PO:0030057)

Moss Ontology definition: Specialized cells at both basal corners of a moss leaf that differ from the other leaf cells in ther size, shape, color or thickness and ornamentation of their walls. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Proposed def.: A plant cell located at the base of a non-vascular leaf adjacent to where the leaf attaches to the stem.

Comment: Found in mosses. Alar cells occur in an area at the base of a leaf that may be triangular, ovate or rectangular and is sometimes called the alar region. They are different in size, shape, color, thickness or ornamentation from other cells in the leaf.

is_a plant cell, part_of non-vascular leaf, part_of leaf base

other refs: Schofeld, Crum, Lars Hedenas The Bryologist 100(1), pp. 65-88.

Blurry image of alar cells at the base of a moss leaf

Accepted

brachycyte (PO:0030058)

Moss Ontology definition: Drought-tolerant cell with thick cell wall developed in protonemata under stress (also called brood cells). A type of gemma. Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary

Proposed def.: A plant cell that develops from a cell in a protonema and has a thick cell wall.

Comment: Found in mosses. A brachycyte is a drought tolerant cell that can act as a gemma and may give rise to a new plant. Cells of a protonema may develop into brachycytes under stress. May form a chain or be separated by tmema cells.

Synonym: brood cell (from Crum)

Accepted

chloronema cell (PO:0030001) and caulonema cell (PO:0030002)

Already added at the POC_Conf._Call_3-8-11.

tmema cell (PO:0030059)

Moss Ontology definition of tmema cell: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

From Crum: An abscission cell at the base of a gemma or brood cell, see also brachytmema and dlichotmema

Proposed def.: A plant cell at the base of a gemma or adjacent to a brachycyte that breaks down to allow abscission of the gemma or brachycyte.

Comment: May be a single cell adjacent to a brachycyte or part of a portion of tmema tissue.

Narrow synonyms: brachytmema cell and dlichotmema cell

Accepted

jacket layer cell (PO:0030052)

Moss Ontology definition: From the unistratose wall of an antheridium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Proposed def. for antheridium jacket layer cell: A plant cell that is part of an antheridium jacket layer.

Synonym: antheridium wall cell

Will add part_of antheridium jacket layer.

Accepted

axillary hair cells

See below, under portions of tissue, for definition of axillary hair.

• gametophore axillary hair terminal cell (PO:0030062)

Moss Ontology definition: A long terminal cell in an axil filament atop a basal stalk. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Proposed def.: A trichome cell that is the long terminal cell of an axillary hair.

part_of gametophore axillary hair

Accepted

• axillary hair base cell

Moss Ontology definition: Basal stalk of an axil filament consisting of two to a dozen cells. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

This actually defines the base of an axillary hair, not a cell. Suggest adding two terms:

Proposed def., gametophore axillary hair base (PO:0030063): A portion of plant tissue that is the basal part of an axillary hair, below the axillary hair terminal cell.

Comment: Consists of two to a dozen cells.

part_of axillary hair

Accepted

Proposed def., gametophore axillary hair basal cell (PO:0030064): A trichome cell that is part of a gametophore axillary hair base.

part_of axillary hair base

Ref: Lars Hedenas The Bryologist 100(1): pp. 65-88.

Accepted

neck canal cell (PO:0030065)

Moss Ontology definition: Cells in the neck of an immature archegonium neck (also called canal cells)

From Crum: The axial row of cells in the neck of an archegonium

Proposed def.: A plant cell that is one of the axial row of cells in an immature archegonium neck.

Comment: As the archegonium matures, the neck canal cells disintegrate to form the neck canal

part_of archegonium neck

Also suggest adding term for archegonium neck canal (PO:0030066): A canal in the center of an archegonium neck.

part_of archegonium neck.

Should rename it "archegonium neck canal cell, and say "archegonium neck canal" in the comment.

Accepted

side branch initial (PO:0030067)

Moss Ontology definition: A single cell produced by the division of sub-apical cells of protonemata. Side branch initials may develop into chloronemata, caulonemata, buds and hence gametophores, or may not divide further. David Cove

Proposed def.: An initial cell that is produced by division of a sub-apical cell of a protonema.

Comment: May give rise to a chloronema, a caulonema, a gametophore bud, or may not divide further.

part_of protonema

Should rename protonema side branch initial.

Accepted

Other cell types, not requested by MO:

• rhizoid initial (PO:0030068)

Proposed def.: An epidermal initial cell that gives rise to a rhizoid. [PMID: 12917289]

Comment: Part of the epidermis of a bryophyte or pteridophyte in the gametophytic phase. May be part of a thallus or gametophore.

participates_in gametophytic phase

Accepted

Note: At the POC_Conf._Call_5-03-11, we decided to make a general class for all types of rhizoids, including those that arise from structures like the protonema that don't have an epidermis. Rhizoids that arise from protonema develop from a protonemal side branch initial. This class rhizoid intial (PO:0030068) should probably be renamed epidermal rhizoid initial. See additional notes at POC_Conf._Call_5-06-11#rhizoids

• hydroid, leptoid, and stereid

hyrdoid (PO:0025032):: An elongate, water conducting cell that is dead at maturity, with tapered ends that are thin and partially hydrolyzed, that lacks specialized wall thickenings or lignin. [source: ISBN:0962073342 (Crum), ISBN:9780717810073]

Comment: Occurs in the gametophytic phase of a plant life cycle.

Proposed def.: A plant cell that is dead at maturity,lacks specialized wall thickenings or lignin, and has tapered ends that are thin and partially hydrolyzed.

Comment: Hydroids are water conducting cells found only in bryophytes, both in the gametophytic phase and in the seta in the sporophytic phase. [source: ISBN:0962073342 (Crum), ISBN:376821110 (Hebant)]

part_of hydrome

Change comment to say "...water and mineral conducting..."

disjoint_from tracheary element

Accepted

leptoid (PO:0025033): A food conducting cell associated with hydroids that resembles the sieve elements of some seedless vascular plants. [source: ISBN:962073342, ISBN:9780717810073]

Comment: Occurs in the gametophytic phase of a plant life cycle.

Proposed def.: A plant cell that resembles in structure the sieve elements of some seedless vascular plants. [ISBN:0962073342, ISBN:376821110]

Comment: A food conducting cell found only in bryophytes in the gametophytic phase and in the seta in the sporophytic phase. Food conducting cells in bryophytes range from conducting parenchyma cells that are indistinguishable from other parenchyma cells to leptoids sensu strictu that are structurally comparable to sieve elements in vascular plants, including many intermediate forms. The term leptoid is used for cells that are distinguishable from parenchyma cells, whether they be intermediate or leptoids sensu strictu.

part_of leptome, disjoint_from sieve tube member

Change comment to say "...carbohydrate and amino acid conducting..." .

Accepted

stereid (PO:0030045): A ground tissue cell with thickened cell walls. [ISBN:0962073342, ISBN:376821110]

Comment: Found only in bryophytes in gametophore axes or non-vascular leaves. Functions in support rather than conduction. May or may not retain a living protoplast at maturity.

part_of stereome

Accepted

Also see separate agenda item for POC_Conf._Call_5-10-11#Conductive cells and tissues for vascular and non-vascular plants

There was some discussion of axial cells and tissues, and of ways to set up the PO so users can compare vascular cells and tissues to their analogs in non-vascular plants. Possibly create a category called something like "vascular cells and analogs". Need to think of a good name, and decide whether or not it is appropriate to group these cells. RW, MAG and DWS have been working on vascular and analogous cells and tissue. For now, the organization should stay as is, in order to get finish edits for the upcoming release, but we can work on re-organizing it for the next release.

Plant Tissues

Postponed until POC_Conf._Call_5-03-11

paraphyllium

Proposed definition: A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.

is_a epidermis, part_of gametophore axis

paraphysis

Proposed def.: A slender, usually uniseriate multicellular trichome that grows intermixed with the gametangia.

Comment: Found in bryophytes and pteridophytes, especially in mosses.

adjacent_to gametangium, plural: paraphyses; particpates_in gametophytic phase

axillary hair (PO:0030060)

Proposed def., gametophore axillary hair: A multicellular trichome consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.

Comment: Found in pleurocarpous mosses. Form in the axils of leaf primordia, and may disappear when the gametophore is mature.

synonym: club-hair; part_of gametophore

rhizoid

Proposed def.: A trichome that is part of a plant in the gametophytic phase and has positive gravitropism.

Comment: Found in bryophytes and pteridopytes growing from the epidermis of the lower surface of a gametophore or thallus. May also arise directly from a protonema. May be muticellular or unicellur. Usually serves to anchor the plant to the substrate.

develops_from rhizoid initial, participates_in gametophytic phase

tmema (PO:0030061)

Proposed def.: A portion of plant tissue that has as parts tmema cells.

Comment: Found in bryophytes at the base of a gemma. Participates in abscission of the gemma.

participates_in gametophytic phase, has_part tmema cell

jacket layer (PO:0030053)

The term jacket layer is also used for the outer layer of sporangia. Suggest naming this term antheridium wall or antheridium jacket layer

proposed definition: A portion of plant tissue that is a single layer of cells on the outside of an antheridium.

Comment: Cells in the antheridium jacket layer surround the inner spermatogenous cells and do not give rise to sperm cells.

part_of antheridium; synonym: sterile jacket layer, antheridium wall

Completion of term requests for Moss Ontology

Plant structures

Archesporium, amphithecium, and endothecium are the only remaining terms to add. See POC_Conf._Call_5-03-11#Parts_of_sporangium on next week's agenda for discussion of these terms.

We have added 54 new terms for bryophytes and related taxa. This includes 35 terms that were directly requested by the Moss Ontology.

There were 24 terms requested by the Moss Ontology that were already in the PO.

The following terms are already in the PO, but should have new synonyms added for bryophytes (PO name followed by synonym):

leaf apex -- phyllid apex

leaf base -- phyllid base

antheridium sperm cell -- spermatozoid

leaf trichome -- phyllid trichome

leaf epidermis -- phyllid epidermis

juvenile leaf -- juvenile phyllid

adult leaf -- adult phyllid

There may be other terms that should have synonyms added, but they were not requested by Moss Ontology

Plant growth and development stages

They have requested about 30 terms, but we told them that would have to wait until we revise the PGDSO.

Upcoming meetings 2011:

Phenotype RCN Meeting: June 1-3rd, Boulder CO PJ will attend More details TBA

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?

*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details