Difference between revisions of "POC Conf. Call 4-26-11"

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In attendance:  
 
In attendance:  
  
−
POC members:   
+
POC members:  Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), ,Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University)
  
−
Absent:
+
Absent: Dennis Stevenson (NYBG),  Chris Mungall (Lawrence Berkeley National Lab),
  
−
Collaborators:  
+
Collaborators: none
  
  
−
Acceptance of the minutes from the [[POC_Conf._Call_4-19-11]]?
+
Acceptance of the minutes from the [[POC_Conf._Call_4-19-11]]? There were no changes, additions or deletions.
  
−
=Issues arising from last week's meeting:=
+
=Summary of Plant Embryo and Embryonic Plant Structure Terms from last week's meeting:=
  
−
=New terms for Physcomitrella and related taxa (continued)=
+
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo (PO:0009009)]==
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 apical cell]==
+
Proposed new def'n: A whole plant in the early part of a sporophytic phase after the first cell division.  
  
−
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'''.
+
new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.
  
 +
''Add to comment: In cultured plant embryos, the embryonic phase ends when organs (roots, shoot axes, or leaves) begin to form.''
  
−
Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.  
+
'''* zygotic plant embryo''' (new term): proposed def'n: A plant embryo that forms as a result of the fusion of gametes.
 +
is_a plant embryo
  
 +
'''* cultured zygote-derived plant embryo'''(new term): proposed def'n: A zygotic plant embryo that is grown or maintained in culture.
 +
synonym: cultured zygotic embryo,  is_a zygotic (plant) embryo, and is_a cultured embryo
  
−
We already have the term '''apical cell (PO:0004000)''', which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." The embryonic apical cell can also be found in non-angiosperms. Suggest obsoleting PO:0004000 and replacing it with the new term'''embryonic apical cell''' for clarity, and using the name '''apical cell''' for the general class of apical cells described below.
+
'''*microspore-derived''' cultured plant embryo (new term): proposed def'n: A cultured plant embryo that develops from isolated microspores.
  
 +
is_a cultured plant embryo,  synonym: microspore-derived haploid embryo
  
−
'''Definition of apical cell from Esau:''' The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
+
'''*somatic plant embryo''' (new term): proposed def'n: A plant embryo that forms as a result of apogamy.
  
−
'''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.
+
Comment: Somatic plant embryo may arise where embryos normally would not arise, i.e. on the edges of leaves on Kalanchoe or ferns,  
  
−
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 the apical cell can give rise to more than two cells (because it can have three or four cutting faces).
+
synonym: adventitious embryo (merge into new term) alt id: PO:0004537
  
 +
'''*Cultured somatic (plant) embryo''' (PO:0000011) def'n: A (plant) embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.
  
−
'''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.
+
''propose revised def'n: A somatic plant embryo arising from previously differentiated somatic cells and grown and maintained in vitro.''
  
−
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 maybe established upon germination of a spore or upon the first cell division of an embryo or later.
+
''is_a somatic plant embryo and also a cultured plant embryo.''
  
−
-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
+
''The above terms and definitions were accepted. Okay to merge adventitious embryo with somatic embryo, but LC will look at it again to make sure.''
  
 +
''Need to look for a good examples of somatic plant embryo -- it may be that Kalanchoe does not form embryos before plantlets form, need to check.''
  
−
Suggested ontology structure for the children of apical cell:
+
''From LC after the meeting:''
  
−
[[File:apical_cell1.jpg]]
+
''According to  George et al , 2008: "Somatic embryogenesis is a process whereby somatic cells differentiate into somatic embryos. Somatic embryos resemble zygotic embryos morphologically. They are bipolar and bear typical embryonic organs. However, they develop via a different pathway. Somatic embryogenesis occurs to a limited extent under natural conditions, within ovules (e.g., Paeonia) and more rarely on leaves (e.g. Asplenium and Kalanchoe)."''
  
−
The dotted lines represent relations inferred by the reasoner.
+
''Further evidence of this was presented by Garces et al, 2007, where they showed that constitutive plantlet-forming species, like Kalanchoë daigremontiana, form plantlets by co-opting both organogenesis and embryogenesis programs into leaves. They present evidence of both morphological and gene expression (LEC1 expression ) similarities to the formation of zygotic embryos.''
  
−
Includes two ways of classifying: 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.
+
''Another example is commonly seen in Citrus, where apomixis occurs - this is perhaps what the original definition of "adventitious embryo" was referring to. (Embryo derived directly from nucellus cells without involving embryo sac cells.) this may be better called "apomitic plant embryo"  There is quite a detailed review by Koltunow, from 1993.''
  
 +
''We may want to reconsider merging the adventitious embryo term into the somatic embryo and rather rename it and make it an is_a  child of.''
  
−
===New terms and definitions for apical cells===
+
''Cited Refs:''
  
 +
''George, E.F., Hall, M.A., and DeKlerk, G.J. (2008). Somatic Embryogenesis. In, The background, Plant propagation by Tissue Culture. Springer SBS, Dordrecht, p. 335–354. (http://www.hos.ufl.edu/mooreweb/tissueculture/february%205/somatic%20embryogenesis.pdf)
  
−
'''gametophytic apical cell (PO:0030014):''' An apical cell that is part of a whole plant in the gametophytic phase.
+
Garcês, H. M. P., Champagne, C. E. M., Townsley, B. T., Park, S., Malhó, R., Pedroso, M. C., Harada, J. J., and Sinha, N. R. (2007). Evolution of asexual reproduction in leaves of the genus Kalanchoë. Proceedings of the National Academy of Sciences, 104, 15578 -15583.
 +
(http://www.pnas.org/content/104/39/15578.full)
  
−
Comment: Occurs bryophytes and pteridophytes.  
+
Koltunow, A. M. (1993). Apomixis: Embryo Sacs and Embryos Formed without Meiosis or Fertilization in Ovules. The Plant Cell Online, 5, 1425 -1437.
 +
(http://www.plantcell.org/content/5/10/1425.full.pdf)''
  
−
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
+
''During the meeting PJ posted this link in the chat: [http://en.wikipedia.org/wiki/Somatic_Embryogenesis#cite_note-Yang-1 Yang] and sent this by email [[File:20-growth_and_development-02-A.pdf‎]]''
  
 +
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]==
  
−
'''sporophytic apical cell (PO:0030015):''' An apical cell that is part of a whole plant in the sporophytic phase.
+
At the [[POC_Conf._Call_4-19-11]] we discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.
  
−
Comment: Occurs in pteridophytes and the sporophyte of bryophytes.  
+
As a solution, we will specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations and develops from relations (e.g., seedling radicle develops_from embryonic radicle). Includes six classes (see below).
  
−
intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase
+
'''* embryonic plant structure''' (PO:0025099): Proposed def'n: A plant structure that is part of an embryo.
  
 +
Comment: Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).
  
−
'''thallus apical cell (PO:0030025):''' An apical cell that is part of a thallus.
 
  
−
part_of thallus
+
''Definition accepted, except should say "plant embryo" instead of "embryo".''
  
 +
''Need to be sure to use "plant embryo" instead of "embryo" in all definitions of descendent terms.''
  
−
'''root apical cell (PO:0030008)''': A sporophytic apical cell that is part of a root apical meristem.
+
''If, at a later point, we add embryonic phase or specific embryonic phases like 8 cell stage or 16 cell stage, we could use participates_in relation to define embryonic structures. However, as we are now defining it, embryonic plant structures should only include structures that are part of an embryo, not structures that are outside the embryo but present during the embryonic phase (like endosperm).''
  
−
comment: Occurs in the sporophytic phase of pteridophytes.
 
  
−
part_of root apical meristem
 
  
 +
===Terms that are is_a children of embryonic plant structure:===
  
−
'''shoot apical cell (PO:0030009)''': An apical cell that is part of a shoot system.
+
'''embryo proper''' (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.
  
−
comment: May occur in shoot axes or leaves of bryophytes or ferns.
+
'''scutellum''' (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
  
−
part_of shoot system
+
'''suspensor''' (PO:0020108): An embryonic plant structure at the base of an embryo that develops from an embryonic basal cell and connects an embryo proper to the wall of a megagametophyte.
  
  
−
'''gametophore apical cell (PO:0030019)''': A shoot apical cell that is part of a gametophore.
+
From DWS: We can also use Singh's "Embryology of Gymnosperms" as a basic reference to create a list of terms that are unique to embryos in gymnosperms.
  
−
comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.
+
===New definitions for embryonic plant cells and tissues===
 +
Both now have cross-product definitions, and no asserted is_a children
  
−
intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
+
'''[http://sourceforge.net/tracker/index.php?func=detail&aid=3177665&group_id=76834&atid=835555 embryonic plant cell]''' (PO:0025028): A plant cell that is part of a plant embryo.
  
 +
-is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
  
−
'''leaf apical cell (PO:0030011)''': A shoot apical cell that is part of a leaf apex.
 
  
−
comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some ferns. Only in plants where leaf growth is apical.
+
*'''embryonic apical cell''' (PO:0030007; replaces apical cell PO:0004000): An embryonic plant cell that is the uppermost cell formed after the first division of a zygote.
  
−
part_of leaf
+
-is_a apical cell; part_of plant embryo (still dev_from zygote).
  
 +
*'''embryonic basal cell''' (formerly: basal cell) (PO:0002002): An embryonic plant cell that is the lower-most cell formed after the first division of a zygote.
  
−
'''non-vascular leaf apical cell (PO:0030013)''': A leaf apical cell that is part of a leaf apex of a non-vascular leaf.
+
-is_a plant cell, part of plant embryo (still dev_from zygote)
  
−
comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
+
*'''embryonic hypophysis''' (formerly hypophysis) (PO:0020109): An embryonic plant cell that is the uppermost cell of the suspensor from which part of the root and root cap in a plant embryo of an angiosperm are derived.  
  
−
part_of non-vasucular leaf; synonym: phyllid apical cell
+
-is_a plant cell, part_of plant embryo.
  
 +
Is it true that this is only in angiosperms? ''Need to check this.''
  
−
'''vascular leaf apical cell (PO:0030012)''': A leaf apical cell that is part of the leaf apex of a vascular leaf.
+
''Although we don't have classes for them yet, we could add terms for any cell that is part of an embryo. For example, 16-cell stage embryonic plant cell would be "A plant cell that is part of an embyro in the 16-cell stage." This would still be inferred to be is_a embryonic plant cell.''
  
−
comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
 
  
−
part_of vascular leaf
+
*'''[https://sourceforge.net/tracker/index.php?func=detail&aid=3293751&group_id=76834&atid=835555 portion of embryonic plant tissue]''' (PO:0025233): A portion of plant tissue that is part of a plant embryo.
  
 +
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of plant embryo
  
−
'''shoot axis apical cell (PO:0030010):''' An apical cell at the tip of a shoot apical meristem.
+
Should we add the '''portion of''' prefix to the name? ''Yes''
  
−
Comment: Divides to produces leaf initial cells and other stem tissues.  
+
* embryo cortex (PO:0005014), embryo endodermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of (portion of) embryonic plant tissue.
  
−
part_of shoot apical meristem
 
  
 +
Here is a picture of some plant tissues, to show how it works:
  
−
'''gametophore axis apical cell (PO:0030023)''': A shoot axis apical cell at the tip of a gametophore axis.
+
[[File:Embryonic plant structure2.jpg]]
  
−
Comment: Occurs at the tips of the stems and branches of bryophytes.
+
''Definitions of embryonic plant cell and portion of embryonic plant tissue were accepted.''
  
−
part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
+
===Proposed changes for structures that were is_a embryonic plant structure:===
  
 +
====structures that only occur in embryos====
  
−
'''vascular shoot axis apical cell (PO:0030024)''': A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.
+
*'''embryo axis''' (PO:0019018): An axial part of an embryo that has as parts a hypocotyl and a root meristem or, if present, a radicle.
  
−
Comment: Occurs in some ferns in their sporophytic phase.
+
'''Proposed definition:''' A plant axis that is the axial part of an embryo.  
  
−
part_of vascular_shoot system; synonym: fern shoot axis apical cell
+
Comment: Has a hypocotyl, root meristem, and radicle as parts, if present.
  
 +
is_a plant axis, part_of embryo
  
−
Also:
+
''Should add zygotic embryo axis as a narrow synonym.''
  
−
'''embryonic apical cell (PO:0025284, replaces PO:0004000)''':  An apical cell that is part of an embryo and is the uppermost cell formed after the first division of a zygote.
 
  
−
Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain meristematic throughout the plant's life.
+
*'''plumule'''(PO:0020032): A somewhat differentiated terminal bud above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.
  
−
==Plant organs:==
+
Comment: Occurs in several embryo types.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]===
+
made is_a terminal bud, part_of embryo
−
- This is the term used for the gametophore stem or axis.
 
  
−
Suggest using '''gametophore axis (PO:0030020)''' as primary name, cauloid as synonym.
 
  
−
'''Proposed def'n:''' A shoot axis that is part of a gametophore.
+
*'''embryonic leaf''' (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].
  
−
Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
+
'''Proposed definition:''' A vascular leaf that is part of an embryo and is one of the first few leaves to develop from the embryonic shoot apical meristem.
  
−
intersection_of: is_a plant axis, intersection_of: part_of gametophore
+
Comment: This term is used to described not yet fully-developed leaves that are part of an embryo.
  
−
Add caulome as synonym of shoot axis
+
is_a vascular leaf, part_of embryo
  
−
-Also suggest adding terms for '''gametophore stem''' and '''gametophore branch'''.
 
  
 +
*'''scutellar node''' (PO:0004708): The region in of an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached. [MaizeGDB:lv]
  
−
'''gametophore stem (PO:0030022)''': A stem that is part of a gametophore.
+
Too vague, because the region between the primary root and the plumule contains the mesocotyl as well as the scutellar node.
  
−
is_a stem, part_of gametophore
+
'''Proposed definition:''' A stem node that is the part of an embryo axis directly above the radicle where the scutellum is attached.
−
 
  
−
'''gametophore branch (PO:0030021)''': A branch that is part of a gametophore.
+
Comment: Found in grasses where no hypocotyl is present. The scutellar node may represent a reduction of the hypocotyl and cotyledonary node. [ref.: Esau 1965]
  
−
is_a branch, part_of gametophore
+
is_a stem node, part_of embryo axis
  
 +
''The changes described above were accepted.''
  
−
-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).
+
====structures that occur in embryos and after embyronic phase====
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract (PO:0030028)]===
+
*'''coleoptile''' (PO:0020033): A tubular (embryonic) plant structure developed at the junction of the cotyledonary sheath with the seedling axis, and surrounding the plumule of a monocot embryo or seedling. [APWeb:Glossary]
  
−
- The specialized phyllids surrounding the antheridia.  
+
We do not have the term cotyledonary sheath in the PO, and, according to Beentje (the Kew Plant Glossary), the coleoptile ''is'' the cotyledonary sheath. Also, the coleoptile persists after germination, so it is not an embryonic plant structure. According to Esau, the coleoptile has stomata, which means it has an epidermis, and this consists of two or more tissue types. This makes it a plant organ, even though many authors casually refer to it as a tissue.
  
−
Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
+
'''Proposed definition:''' A phyllome that surrounds the plumule of an embryo or the emerging shoot apex of a seedling. [ISBN:9781842464229, ISBN: 0471244554]
  
−
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.
+
Comment: Found in Poaceae. Develops at the first node above the scutellum, and thus is often thought to be the first leaf. Protects the emerging shoot system as it grows through the soil.
  
−
'''Proposed def'n:''' A bract that subtends an antheridium.  
+
Note: A phyllome is "a lateral plant organ produced by a shoot apical meristem."
  
−
part_of gametophore, participates in gametophytic phase
+
'''New children:'''
  
−
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.
+
'''embryonic coleoptile (PO:0025286)''': A coleoptile that is part of a plant embryo.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3234965&group_id=76834&atid=835555 foot]===
+
'''seedling coleoptile (PO:0025287)''': A coleoptile that is part of a whole plant in the seedling phase.
  
−
Moss Ontology definition: The base of the sporophytes in mosses
+
(can't add participates in seedling phase yet) develops_from embryonic coleoptile
  
−
'''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)
+
''It was suggested that we define the coleoptile as the first plastichron to form from the embryonic shoot apical meristem.''
  
−
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)
+
''RW after meeting: We don't have plastichron in the PO, and the term is generally used for measuring the age of plants based on the number of leaves produced. May be better to say it is the first phyllome formed.''
  
−
participates_in sporophytic phase, has_part transfer cell
+
''New proposed comment: Found in Poaceae. The coleoptile is the first phyllome formed from the embryonic shoot apical meristem. Protects the emerging shoot system as it grows through the soil.''
  
−
==Additional organ related moss terms:==
+
''New definition for seedling coleoptile: A coleoptile that develops from an embryonic coleoptile. Comment: A seedling coleoptile is an elongation of an embryonic coleoptile and is part of a whole plant in the seedling phase.''
  
−
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.
+
''Use similar wording for other seedling structures.''
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perichaetal bract (PO:0030030)]===
 
  
−
'''Proposed def.:''' A bract that subtends an archegonium. part_of gametophore
+
*'''coleorhiza''' (PO:0020034): A portion of plant tissue surrounding the radicle in the embryo or seedling of some monocots. [APWeb:Glossary]
  
−
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.
+
Currently part_of embryo, but it is also part of the seedling. It develops in the embryo, but persists after germination to protect the embryonic root. The coleorhiza, like the coleoptile, has an epidermis (and root hairs), and thus should be classified as a plant organ, even though many authors casually refer to it as a tissue.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth (PO:0030031)]===
+
'''Proposed definition:''' A plant organ that surrounds the radicle in the embryo and seedling.
  
−
'''Proposed def.:'''  A collective phyllome structure that consists of two or more of the most distal perichaetal bracts on a gametophore axis and surround a capsule.
+
Comment: Found in Poaceae and some other monocots. Protects the emerging embryonic root. The parenchyma cells of both the coleorhiza and epiblast may function in storage.
  
 +
'''New children:'''
  
−
-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)
+
'''embryonic coleorhiza (PO:0025288)''': A coleorhiza that is part of a plant embryo.
  
−
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.
+
'''seedling coleorhiza (PO:0025289)''': A coleorhiza that is part of a whole plant in the seedling phase.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185175&group_id=76834&atid=835555 seta (PO:0030032)]===
+
(can't add participates in seedling phase yet) develops_from embryonic coleorhiza
  
−
-The stalk of a moss sporophyte.
 
  
−
'''Proposed def.:''' A plant axis that holds up a spore capsule. participates_in sporophytic phase
+
*'''hypocotyl''' (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]
  
−
Comment: Found in some bryophytes, especially mosses.
+
currently is_a cardinal organ part, propose is_a stem internode (we didn't have this term before but do now)
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3272612&group_id=76834&atid=835555 antheridiophore and archegoniophore]===
+
'''Proposed definition:''' A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.
  
−
These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)
+
is_a stem internode
  
−
'''Proposed definitions:'''
+
'''New children:'''
  
−
'''antheridiophore (PO:0030033):''' A plant axis that bears two or more antheridia.
+
'''embryonic hypocotyl (PO:0025290)''': A hypocotyl that is part of a plant embryo.
  
−
participates_in gametophytic phase
+
'''seedling hypocotyl (PO:0025291)''': A hypocotyl that is part of a whole plant in the seedling phase.
  
−
Comment: Antheridia are borne on a disk-shaped archegonial head. Found in Marchantiales.
+
(can't add participates in seedling phase yet) develops_from embryonic hypocotyl
  
−
'''archegoniophore (PO:0030034):''' A plant axis that bears two or more archegonia.
+
''Some discussion of hypocotyl hook or apical hook. We already have the term PO:0000012 (apical hook, synonym hypocotyl hook), part_of hypocotyl.
  
−
participates_in gametophytic phase
 
  
−
Comment: Archegonia are borne on an umbrella-shaped archegonial head. Found in Marchantiales.
+
*'''hypocotyl-root junction''' (PO:0004724): A cardinal organ part that is the part of a plant axis where a radicle joins a hypocotyl.
  
 +
Moved to is_a cardinal organ part.
  
−
Will also add terms for '''antheridium stalk (PO:0030035)''' and '''archegonium stalk (PO:0030036)''':
+
'''Proposed definition:''' A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.
  
−
A stalk that the basal part of an antheridium/archegonium. part_of antheridium or archegonium.
+
synonym: embryo axis transition zone (Bell and Bryan 2008, and others)
  
−
Comment: Raises the antheridium/venter above the rest of the gametophyte.
+
'''New children:'''
  
−
==Cardinal organ parts==
+
'''embryonic hypocotyl-root junction (PO:0025300)''': A hypocotyl-root junction that is part of an embryo axis.
−
Terms requested by MO:
 
  
−
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234979&group_id=76834&atid=835555 calyptra]'''
+
'''seedling hypocotyl-root junction (PO:0025301)''': A hypocotyl-root junction that is part of a whole plant in the seedling phase.
  
−
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.
+
(can't add participates in seedling phase yet) develops_from embryonic hypocotyl-root junction
  
−
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.
+
''Add Poaceae crown as narrow synonym of hypocotyl-root junction.''
  
−
'''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.
+
*'''epicotyl''' (PO:0020035): The first internode of a stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. [APWeb:Glossary]
  
−
participates_in gametophytic phase, develops_from archegonium
+
currently is_a embryonic plant structure, propose is_a stem internode (PO:0005005). Also, the second part of the current definition only adds ambiguity. Need to define it more precisely.
  
−
subsets for bryophytes, pteridophytes
+
'''Proposed definition:''' The first stem internode above a hypocotyl. [Esau]
  
 +
Comment: The epicotyl is the first internode of a stem above the cotyledons.
  
 +
'''New children:'''
  
−
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234981&group_id=76834&atid=835555 venter (PO:0030038)]'''
+
'''embryonic epicotyl (PO:0025292)''': A epicotyl that is part of a plant embryo.
  
−
This term was not suggested by Moss Ontology, but perhaps we should add it.
+
'''seedling epicotyl (PO:0025293)''': A epicotyl that is part of a whole plant in the seedling phase.
  
−
'''proposed def.:''' A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.
+
(can't add participates in seedling phase yet) develops_from embryonic epicotyl
  
−
part_of archegonium
 
  
−
subsets for bryophytes, pteridophytes, gymnosperms
+
*'''mesocotyl''' (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.
  
 +
This definition sounds like the same thing as an epicotyl. Esau says the mesocotyl is the plant axis between the scutellum and the coleoptile and that in grasses, the scutellum is generally thought to  represent the cotyledon and the coleoptile to represent the first leaf. In that case, the mesocotyl (as the axis between the scutellum and the coleoptile), is analogous (or homologous) to the epicotyl in dicots and other monocots. In grasses, the hypocotyl is not visible, except perhaps as the scutellar node.
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3234985&group_id=76834&atid=835555 archegonium neck(PO:0030039)]'''
+
For a picture, see http://www.agry.purdue.edu/ext/corn/news/timeless/GerminationEvents.html
  
−
This term was not suggested by Moss Ontology, but perhaps we should add it.
+
'''Proposed definition:''' A shoot internode that is the part of an embryo axis or the stem of a seedling above the scutellum and below the coleoptile. [Easu]
  
−
'''proposed def.:''' A cardinal organ part that is the elongated apical part of an archegonium.
+
Comment: Occurs in grasses. In grasses, the hypocotyl and cotyledon may not be visible and may be represented by the scutellar node and scutellum, making the mesocotyl similar to the epicotyl in other taxa. Elongation of the mesocotyl during seedling growth pushes the coleoptile above the soil surface.
  
−
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.
+
'''New children:'''
  
−
part_of archegonium
+
'''embryonic mesocotyl (PO:0025294)''': A mesocotyl that is part of a plant embryo.
  
−
(can also add term for neck canal cell when we deal with cells)
+
'''seedling mesocotyl (PO:0025295)''': A mesocotyl that is part of a whole plant in the seedling phase.
  
−
subsets for bryophytes, pteridophytes, gymnosperms
+
(can't add participates in seedling phase yet) develops_from embryonic mesocotyl
  
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241725&group_id=76834&atid=835555 base]'''
+
*'''embryonic root''' (PO:0000045): A root that is initiated in a developing embryo. [TAIR:ki]
  
−
'''Proposed name and def.: sporangium base (PO:0030040)''': A cardinal organ part that is the basal part of a sporangium.
+
Embryonic root is not part_of embryo (at present). Has children '''radicle''' (PO:0020031) and '''seminal root''' (PO:0000046).  
  
−
Comment:  Term used in mosses and other bryophytes (what about 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)
+
Will need to revisit this when we look at organization of root (PO:0009005)
  
−
part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
 
  
−
subsets for bryophytes
+
*'''radicle''' (PO:0020031): The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive. is_a embryonic root [APWeb:Glossary]
  
 +
'''Proposed definition:''' An embryonic root that is the basal continuation of a hypocotyl in an embryo. 
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241737&group_id=76834&atid=835555 theca]'''
+
Comment: May develop into the root system of an adult plant. Sometimes abortive.
  
−
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
+
Primary root (PO:0020127) develops from radicle.
  
−
We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that '''anther theca''' and call this term '''sporangium theca:'''.
+
'''New children:'''
  
−
'''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.
+
'''embryonic radicle (PO:0025296)''': A radicle that is part of a plant embryo.
  
−
Comment: Term used for bryophytes and pteridophytes.
+
'''seedling radicle (PO:0025297)''': A radicle that is part of a whole plant in the seedling phase.
  
−
part_of sporangium
+
(can't add participates in seedling phase yet) develops_from embryonic radicle
  
−
subsets for bryophytes, pteridophytes
 
  
 +
''Except as noted above, the above definitions were accepted. Will reword the definitions of all of the seedling terms to reflect that they develop from the embryonic structures and post on Source Forge''
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241747&group_id=76834&atid=835555 peristome (PO:0030042)]'''
+
=New terms for Physcomitrella and related taxa (continued)=
  
−
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
+
==Collective plant structures:==
  
−
'''proposed definition:''' A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore (PO:0030018)]===
  
−
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.
+
Definition supplied by Moss Ontology: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.
  
−
part_of sporangium
+
Suggest is_a shoot system.
  
−
subsets for bryophytes
+
'''Proposed def.:''' A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.
  
 +
participates_in gametophytic phase, develops_from gametophore bud
  
−
*'''peristome tooth (PO:0030043)'''
+
Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.
  
−
Not requested by Moss Ontology, but should add it.
+
subset for bryophytes
  
−
'''Proposed def:''' A cardinal organ part that is a single lobe or tooth of a peristome.
+
''Accepted''
  
−
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud (PO:0030026)]===
  
−
part_of peristome
+
The term "bud" has been requested:
 +
Def'n supplied by Moss Ontology: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove
  
−
subsets for bryophytes
+
Suggest a new term '''gametophore bud'''. This could be a child of bud (PO:0000055: An undeveloped shoot system).
  
 +
'''Proposed def'n:''' A vegetative bud that develops into a gametophore.
  
−
*Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
+
Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
  
 +
participates_in gametophytic phase, has_part gametophore apical cell
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241767&group_id=76834&atid=835555 lid/operculum]'''
+
synonym: brown bud
  
−
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.
+
''Accepted''
  
−
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.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus (PO:0030027)]===
  
−
'''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.
+
From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.
  
−
Comment: Found in mosses. May remain partly attached to the rest of the capsule.
+
From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.
  
−
Synonym: sporangium lid
 
  
−
part_of sporangium
+
Saying a thallus is a gametophore implies that it is a shoot system and therefore a collective plant structure (CPS). As a CPS, it must have more that one organ. This is not true for a thallus (sometime they branch, so you could say they have multiple axes, but it is a stretch. Maybe better to classify it as a whole plant.
  
−
subsets for bryophytes
 
  
−
===Also add these terms for angiosperms:===
+
'''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
  
−
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 fruit operculum]:''' A collective organ part structure that is the apical part of a circumsesile capsular fruit that separates from the rest of the capsule during dehiscence.
+
Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
  
−
Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.
 
  
−
part_of fruit
+
Add '''prothallium''' as a broad synonym of thallus and as a narrow synonym of whole plant.
  
−
Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
+
''Accepted''
  
 +
===Other gametophyte terms===
  
−
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 perianth calyptra]:''' A perianth that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.  
+
We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.
  
−
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.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 apical cell]==
  
−
==Other related terms for mosses, not from Moss Ontology==
+
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'''.
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241816&group_id=76834&atid=835555 spore capsule mouth]'''
 
  
−
'''Proposed definition:''' A plant anatomical space that is the opening on the apical end of a spore capsule.
+
Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.  
  
−
Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
 
  
−
part_of sporangium
+
We already have the term '''apical cell (PO:0004000)''', which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." The embryonic apical cell can also be found in non-angiosperms. Suggest obsoleting PO:0004000 and replacing it with the new term '''embryonic apical cell''' for clarity, and using the name '''apical cell''' for the general class of apical cells described below.
  
−
subsets for bryophytes
 
  
 +
'''Definition of apical cell from Esau:''' The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241820&group_id=76834&atid=835555 epiphragm]'''
+
'''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.
  
−
Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
+
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 the apical cell can give rise to more than two cells (because it can have three or four cutting faces).  
  
−
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 collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.  
+
'''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: Present in some moss species of the family Polytrichaceae.
+
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.
  
−
Synonym: tympanum, epiphram
+
-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
  
−
subsets for bryophytes
+
''There was some discussion 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. Will review definition at next meeting.''
  
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241827&group_id=76834&atid=835555 pseudopodium]'''
+
Suggested ontology structure for the children of apical cell:
  
−
From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
+
[[File:apical_cell1.jpg]]
  
−
From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
+
The dotted lines represent relations inferred by the reasoner.
  
−
'''Proposed definition:''' A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
+
Includes two ways of classifying: 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.
  
−
Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
+
''This ontology structure was approved.''
  
−
participates_in gametophytic phase
+
''During the meeting PJ posted this link in the chat: [http://www.annualreviews.org/doi/full/10.1146/annurev.arplant.48.1.673 SAM Review]
  
−
subsets for bryophytes
+
===New terms and definitions for apical cells===
  
 +
''Definitions for the descendents of apical cell were approved, pending approval of final definition of apical cell.''
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3132600&group_id=76834&atid=835555 Sporangium]==
+
'''gametophytic apical cell (PO:0030014):''' An apical cell that is part of a whole plant in the gametophytic phase.
  
−
We currently have the class '''sporangium''' (PO:0025094), which is a cardinal organ part.  
+
Comment: Occurs bryophytes and pteridophytes.  
  
−
'''Current def:''' A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]
+
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
  
−
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. Would it be legitimate to say that in seed plants, the sporangium is a reduced organ that is located in another organ? If so, could change the parent to plant organ.
+
'''sporophytic apical cell (PO:0030015):''' An apical cell that is part of a whole plant in the sporophytic phase.
  
−
Is it really hollow? It is full of sporocytes or spores.
+
Comment: Occurs in pteridophytes and the sporophyte of bryophytes.  
  
 +
intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase
  
−
'''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 unicellular in some algae.  
+
'''thallus apical cell (PO:0030025):''' An apical cell that is part of a thallus.  
  
 +
part_of thallus
  
−
We also have:
 
  
−
'''megasporangium''' (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]
+
'''root apical cell (PO:0030008)''': A sporophytic apical cell that is part of a root apical meristem.
  
−
'''microsporangium''' (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]
+
comment: Occurs in the sporophytic phase of pteridophytes.
  
−
'''nucellus''' (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]
+
part_of root apical meristem
  
−
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]
+
'''shoot apical cell (PO:0030009)''': An apical cell that is part of a shoot system.
  
−
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.
+
comment: May occur in shoot axes or leaves of bryophytes or ferns.
  
 +
part_of shoot system
  
−
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 ''located in'' an ovule and surrounding a megasporocyte.  
+
'''gametophore apical cell (PO:0030019)''': A shoot apical cell that is part of a gametophore.
  
−
'''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]
+
comment: Occurs in the non-vascular shoot system of the gametophyte of mosses and leafy liverworts.
  
−
(comments stay the same)
+
intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
  
−
We could continue to use the more general part_of relation for located_in, if we don't want to add a new relation.
 
  
−
==Plant Cells==
+
'''leaf apical cell (PO:0030011)''': A shoot apical cell that is part of a leaf apex.
  
−
Terms requested by Moss Ontology:
+
comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some ferns. Only in plants where leaf growth is apical.
  
−
===archesporial cell===
+
part_of leaf apex
  
−
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]
+
'''non-vascular leaf apical cell (PO:0030013)''': A leaf apical cell that is part of a leaf apex of a non-vascular leaf.
  
−
'''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]
+
comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
  
 +
part_of non-vasucular leaf; synonym: phyllid apical cell
  
  
−
Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.
+
'''vascular leaf apical cell (PO:0030012)''': A leaf apical cell that is part of the leaf apex of a vascular leaf.
  
−
'''Proposed definitions:'''
+
comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
  
−
'''archesporial cell''' A plant cell that divides to gives rise to a sporocyte and is part of a sporangium.
+
part_of vascular leaf
  
−
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
+
'''shoot axis apical cell (PO:0030010):''' An apical cell at the tip of a shoot apical meristem.
  
 +
Comment: Divides to produces leaf initial cells (if leaves are present) and other stem or branch tissues.
  
−
'''female archesporial cell''' (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.
+
part_of shoot apical meristem
  
−
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]
 
−
 
  
−
'''male archesporial cell''' (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.
+
'''gametophore axis apical cell (PO:0030023)''': A shoot axis apical cell at the tip of a gametophore axis.
  
−
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]
+
Comment: Occurs at the tips of the stems and branches of bryophytes.
  
−
===alar cell===
+
part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
−
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 form other cells in the leaf.
+
'''vascular shoot axis apical cell (PO:0030024)''': A shoot axis apical cell at the tip of a shoot apical meristem in a shoot system that has as part vascular tissue.
  
−
is_a plant cell, part_of non-vascular leaf, part_of leaf base
+
Comment: Occurs in some ferns in their sporophytic phase.
  
−
other refs: Schofeld, Crum, Lars Hedenas The Bryologist 100(1), pp. 65-88.
+
participates_in sporophytic phase; synonym: fern shoot axis apical cell
  
  
−
[[File:alar_cell.jpg]] Blurry image of alar cells at the base of a moss leaf
+
'''seta apical cell (PO:0030016)''': A shoot axis apical cell at the tip of a seta.
  
−
===brachycyte===
+
Comment: Ceases being an apical cell when the sporangium begins to develop.
  
−
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
+
part_of seta
  
−
'''Proposed def.:''' A plant cell that develops from a cell in a protonema and has a thick cell wall.
+
Also:
  
−
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.
+
'''embryonic apical cell (PO:0025284, replaces PO:0004000)''': An apical cell that is part of a plant embryo and is the uppermost cell formed after the first division of a zygote.
  
−
Synonym: brood cell (from Crum)
+
Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain meristematic throughout the plant's life.
−
 
 
−
===chloronema cell (PO:0030001) and caulonema cell (PO:0030002)===
 
−
 
 
−
Already added at the [[POC_Conf._Call_3-8-11]].
 
−
 
 
−
===tmema cell===
 
−
 
 
−
Moss Ontology definition: 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.
 
−
 
 
−
===jacket layer cell===
 
−
 
 
−
Moss Ontology definition: From the unistratose wall of an antheridium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 
−
 
 
−
We can address the definition of jacket layer (aka sporangium wall) when we deal with the parts of a sporangium but assuming that the sporangium wall exists, we can add this cell term now.
 
−
 
 
−
'''Proposed def. for sporangium wall cell:'''A plant cell that is part of a sporangium wall.
 
−
 
 
−
Comment: The sporangium wall is also known as the jacket layer.
 
−
 
 
−
Synonym: sporangium jacket layer cell
 
−
 
 
−
===axillary hair cells===
 
−
 
 
−
See below, under portions of tissue, for definition of '''axillary hair'''.
 
−
 
 
−
*'''axillary hair terminal cell'''
 
−
 
 
−
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 plant (epidermal?) cell that is the long terminal cell of an axillary hair.
 
−
 
 
−
part_of axillary hair
 
−
 
 
−
 
 
−
*'''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., axillary hair base:''' A portion of plant (epidermal?) 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
 
−
 
 
−
 
 
−
'''Proposed def., axillary hair basal cell:''' A plant (epidermal?) cell that is part of an axillary hair base.
 
−
 
 
−
part_of axillary hair base
 
−
 
 
−
 
 
−
Lars Hedenas The Bryologist 100(1), pp. 65-88.
 
−
 
 
−
===neck canal cell===
 
−
 
 
−
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 dissintegrate to form the neck canal
 
−
 
 
−
part_of archegonium neck, synonym: canal cell
 
−
 
 
−
 
 
−
Also suggest adding term for '''neck canal:''' A canal that in the center of an archegonium neck.
 
−
 
 
−
part_of archegonium neck.
 
−
 
 
−
===side branch initial===
 
−
 
 
−
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 buse, or may not divide further.
 
−
 
 
−
part_of protonema
 
−
 
 
−
===Other cell types, not requested by MO:===
 
−
 
 
−
*'''rhizoid initial'''
 
−
 
 
−
'''Proposed def.:''' An epidermal initial cell that gives rise to a rhizoid. [PMID: 12917289]
 
−
 
 
−
part_of gametophore epidermis
 
−
 
 
−
 
 
−
*'''hydroids and leptoids'''
 
−
 
 
−
See separate agenda for [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-28-11#Conductive_cells_and_tissue conductive cells and tissues]
 
−
 
 
−
==Plant Tissues==
 
−
 
 
−
===paraphyllium===
 
−
 
 
−
Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
 
  
−
Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."
+
=Review for OBO Foundry Acceptance=
  
−
Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
+
At last weeks meeting, BS suggested that the PO can be submitted for OBO Foundry membership within the next weeks
  
−
Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.
+
By email after the call: BS sent us a link to the list of principles: [[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles OBO_Foundry_Principles]] and then CM sent:"Use the list here":  [[http://www.obofoundry.org/wiki/index.php/Category:Accepted Accepted]]
  
−
'''Proposed definition:''' A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.
+
Which one is the one to use?
  
−
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.
+
=Upcoming meetings 2011:=
  
−
[[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
+
'''[http://www.iplantcollaborative.org/2011/02/09/2011-semantic-web-workshop-june-6-7-santa-fe-nm 2011 Semantic Web Workshop] June 6th and 7th, Santa Fe, NM.  
 +
'''
  
−
===paraphysis===
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
  
−
Moss Ontology definition: Sterile, septate, usually uniseriate hairs intermixed with sex organs. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
+
-JE and JP will be attending
  
−
From Parihar: sterile, slender filaments accompanying reproductive organs.
+
-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.  
  
−
From Schofeld: filamentous sterile structures intermixed with the sex organs of most mosses
+
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
  
−
'''Proposed def.:''' A portion of plant tissue that is a slender, usually uniseriate hair-like structure that grows intermixed with the gametangia.
+
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30, 2011
 +
Buffalo, New York
  
−
Comment: Found in bryophytes and pteridophytes, especially in mosses.
+
[http://icbo.buffalo.edu ICBO]
  
−
adjacent_to gametangium, plural: paraphyses
+
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.
  
−
===axilliary hair===
+
'''Full-Day Workshops Schedule:'''
  
−
Moss Ontology definition: A small filament in an axil consisting of one long terminal cell atop a basal stalk (also called club-hair). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
+
'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
Is it a type of trichome?
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
'''Proposed def.:''' A trichome (''or portion of plant tissue'') consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.
+
'''July 26 6.30pm-9pm''' Evening Workshop: Common Logic
  
−
Comment: Found in pleurocarpous mosses.
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
−
synonym: club-hair
+
- LC will attend and represent the PO.  Invite other plant people?
  
−
===rhizoid===
 
  
−
Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.
 
  
−
Rhizoids may also grow from thalli. They arise from the epidermis, and so are like trichomes. Like trichomes, they may be uni- or multicellur
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
 +
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
−
'''Proposed def.:''' A trichome that grows from the epidermis of a plant in the gametophytic phase.
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
−
Comment: Found in bryophytes and pteridopytes growing from a gametophore or thallus. May be muticellular or unicellur. May anchor the plant to the substrate.
+
Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.
  
−
===tmema===
+
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
  
−
Moss Ontology definition: 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
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
−
Their definition defines a cell type, but they have tmema as a tissue type. It would be the tissue composed of tmema cells
 
  
−
'''Proposed def.:''' A portion of plant tissue composed of tmema cells.
 
  
−
Comment: Found in bryophytes at the base of a gemma or a brachycyte that will act as a gemma. Participates in abscission of the gemma.
+
'''* International Botanical Congress (IBC2011)'''
  
−
===archesporium, amphithecium, endothecium, jacket layer===
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
See separate agenda item for [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-28-11#Sporangium_parts parts of sporangium].
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]  
  
−
sporogenous tissue or archesporium
+
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.
  
−
===Conductive tissue===
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
  
−
See separate agenda for [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-28-11#Conductive_cells_and_tissue conductive cells and tissues]
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
 
=Next meeting scheduled for Thur, April 28th, 2011 at 10am PDT=
 
=Next meeting scheduled for Thur, April 28th, 2011 at 10am PDT=

Latest revision as of 13:19, 20 May 2011

POC meeting, Webex Conference Call; Date: Tuesday Apr 26th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), ,Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University)

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab),

Collaborators: none


Acceptance of the minutes from the POC_Conf._Call_4-19-11? There were no changes, additions or deletions.

Summary of Plant Embryo and Embryonic Plant Structure Terms from last week's meeting:

plant embryo (PO:0009009)

Proposed new def'n: A whole plant in the early part of a sporophytic phase after the first cell division.

new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.

Add to comment: In cultured plant embryos, the embryonic phase ends when organs (roots, shoot axes, or leaves) begin to form.

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

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

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

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

*somatic plant embryo (new term): proposed def'n: A plant embryo that forms as a result of apogamy.

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

synonym: adventitious embryo (merge into new term) alt id: PO:0004537

*Cultured somatic (plant) embryo (PO:0000011) def'n: A (plant) embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.

propose revised def'n: A somatic plant embryo arising from previously differentiated somatic cells and grown and maintained in vitro.

is_a somatic plant embryo and also a cultured plant embryo.

The above terms and definitions were accepted. Okay to merge adventitious embryo with somatic embryo, but LC will look at it again to make sure.

Need to look for a good examples of somatic plant embryo -- it may be that Kalanchoe does not form embryos before plantlets form, need to check.

From LC after the meeting:

According to George et al , 2008: "Somatic embryogenesis is a process whereby somatic cells differentiate into somatic embryos. Somatic embryos resemble zygotic embryos morphologically. They are bipolar and bear typical embryonic organs. However, they develop via a different pathway. Somatic embryogenesis occurs to a limited extent under natural conditions, within ovules (e.g., Paeonia) and more rarely on leaves (e.g. Asplenium and Kalanchoe)."

Further evidence of this was presented by Garces et al, 2007, where they showed that constitutive plantlet-forming species, like Kalanchoë daigremontiana, form plantlets by co-opting both organogenesis and embryogenesis programs into leaves. They present evidence of both morphological and gene expression (LEC1 expression ) similarities to the formation of zygotic embryos.

Another example is commonly seen in Citrus, where apomixis occurs - this is perhaps what the original definition of "adventitious embryo" was referring to. (Embryo derived directly from nucellus cells without involving embryo sac cells.) this may be better called "apomitic plant embryo" There is quite a detailed review by Koltunow, from 1993.

We may want to reconsider merging the adventitious embryo term into the somatic embryo and rather rename it and make it an is_a child of.

Cited Refs:

George, E.F., Hall, M.A., and DeKlerk, G.J. (2008). Somatic Embryogenesis. In, The background, Plant propagation by Tissue Culture. Springer SBS, Dordrecht, p. 335–354. (http://www.hos.ufl.edu/mooreweb/tissueculture/february%205/somatic%20embryogenesis.pdf)

Garcês, H. M. P., Champagne, C. E. M., Townsley, B. T., Park, S., Malhó, R., Pedroso, M. C., Harada, J. J., and Sinha, N. R. (2007). Evolution of asexual reproduction in leaves of the genus Kalanchoë. Proceedings of the National Academy of Sciences, 104, 15578 -15583. (http://www.pnas.org/content/104/39/15578.full)

Koltunow, A. M. (1993). Apomixis: Embryo Sacs and Embryos Formed without Meiosis or Fertilization in Ovules. The Plant Cell Online, 5, 1425 -1437. (http://www.plantcell.org/content/5/10/1425.full.pdf)

During the meeting PJ posted this link in the chat: Yang and sent this by email File:20-growth and development-02-A.pdf

embryonic plant structures

At the POC_Conf._Call_4-19-11 we discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.

As a solution, we will specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations and develops from relations (e.g., seedling radicle develops_from embryonic radicle). Includes six classes (see below).

* embryonic plant structure (PO:0025099): Proposed def'n: A plant structure that is part of an embryo.

Comment: Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle).


Definition accepted, except should say "plant embryo" instead of "embryo".

Need to be sure to use "plant embryo" instead of "embryo" in all definitions of descendent terms.

If, at a later point, we add embryonic phase or specific embryonic phases like 8 cell stage or 16 cell stage, we could use participates_in relation to define embryonic structures. However, as we are now defining it, embryonic plant structures should only include structures that are part of an embryo, not structures that are outside the embryo but present during the embryonic phase (like endosperm).


Terms that are is_a children of embryonic plant structure:

embryo proper (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.

scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.

suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from an embryonic basal cell and connects an embryo proper to the wall of a megagametophyte.


From DWS: We can also use Singh's "Embryology of Gymnosperms" as a basic reference to create a list of terms that are unique to embryos in gymnosperms.

New definitions for embryonic plant cells and tissues

Both now have cross-product definitions, and no asserted is_a children

embryonic plant cell (PO:0025028): A plant cell that is part of a plant embryo.

-is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo


  • embryonic apical cell (PO:0030007; replaces apical cell PO:0004000): An embryonic plant cell that is the uppermost cell formed after the first division of a zygote.

-is_a apical cell; part_of plant embryo (still dev_from zygote).

  • embryonic basal cell (formerly: basal cell) (PO:0002002): An embryonic plant cell that is the lower-most cell formed after the first division of a zygote.

-is_a plant cell, part of plant embryo (still dev_from zygote)

  • embryonic hypophysis (formerly hypophysis) (PO:0020109): An embryonic plant cell that is the uppermost cell of the suspensor from which part of the root and root cap in a plant embryo of an angiosperm are derived.

-is_a plant cell, part_of plant embryo.

Is it true that this is only in angiosperms? Need to check this.

Although we don't have classes for them yet, we could add terms for any cell that is part of an embryo. For example, 16-cell stage embryonic plant cell would be "A plant cell that is part of an embyro in the 16-cell stage." This would still be inferred to be is_a embryonic plant cell.


is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of plant embryo

Should we add the portion of prefix to the name? Yes

  • embryo cortex (PO:0005014), embryo endodermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of (portion of) embryonic plant tissue.


Here is a picture of some plant tissues, to show how it works:

Embryonic plant structure2.jpg

Definitions of embryonic plant cell and portion of embryonic plant tissue were accepted.

Proposed changes for structures that were is_a embryonic plant structure:

structures that only occur in embryos

  • embryo axis (PO:0019018): An axial part of an embryo that has as parts a hypocotyl and a root meristem or, if present, a radicle.

Proposed definition: A plant axis that is the axial part of an embryo.

Comment: Has a hypocotyl, root meristem, and radicle as parts, if present.

is_a plant axis, part_of embryo

Should add zygotic embryo axis as a narrow synonym.


  • plumule(PO:0020032): A somewhat differentiated terminal bud above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.

Comment: Occurs in several embryo types.

made is_a terminal bud, part_of embryo


  • embryonic leaf (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].

Proposed definition: A vascular leaf that is part of an embryo and is one of the first few leaves to develop from the embryonic shoot apical meristem.

Comment: This term is used to described not yet fully-developed leaves that are part of an embryo.

is_a vascular leaf, part_of embryo


  • scutellar node (PO:0004708): The region in of an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached. [MaizeGDB:lv]

Too vague, because the region between the primary root and the plumule contains the mesocotyl as well as the scutellar node.

Proposed definition: A stem node that is the part of an embryo axis directly above the radicle where the scutellum is attached.

Comment: Found in grasses where no hypocotyl is present. The scutellar node may represent a reduction of the hypocotyl and cotyledonary node. [ref.: Esau 1965]

is_a stem node, part_of embryo axis

The changes described above were accepted.

structures that occur in embryos and after embyronic phase

  • coleoptile (PO:0020033): A tubular (embryonic) plant structure developed at the junction of the cotyledonary sheath with the seedling axis, and surrounding the plumule of a monocot embryo or seedling. [APWeb:Glossary]

We do not have the term cotyledonary sheath in the PO, and, according to Beentje (the Kew Plant Glossary), the coleoptile is the cotyledonary sheath. Also, the coleoptile persists after germination, so it is not an embryonic plant structure. According to Esau, the coleoptile has stomata, which means it has an epidermis, and this consists of two or more tissue types. This makes it a plant organ, even though many authors casually refer to it as a tissue.

Proposed definition: A phyllome that surrounds the plumule of an embryo or the emerging shoot apex of a seedling. [ISBN:9781842464229, ISBN: 0471244554]

Comment: Found in Poaceae. Develops at the first node above the scutellum, and thus is often thought to be the first leaf. Protects the emerging shoot system as it grows through the soil.

Note: A phyllome is "a lateral plant organ produced by a shoot apical meristem."

New children:

embryonic coleoptile (PO:0025286): A coleoptile that is part of a plant embryo.

seedling coleoptile (PO:0025287): A coleoptile that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic coleoptile

It was suggested that we define the coleoptile as the first plastichron to form from the embryonic shoot apical meristem.

RW after meeting: We don't have plastichron in the PO, and the term is generally used for measuring the age of plants based on the number of leaves produced. May be better to say it is the first phyllome formed.

New proposed comment: Found in Poaceae. The coleoptile is the first phyllome formed from the embryonic shoot apical meristem. Protects the emerging shoot system as it grows through the soil.

New definition for seedling coleoptile: A coleoptile that develops from an embryonic coleoptile. Comment: A seedling coleoptile is an elongation of an embryonic coleoptile and is part of a whole plant in the seedling phase.

Use similar wording for other seedling structures.


  • coleorhiza (PO:0020034): A portion of plant tissue surrounding the radicle in the embryo or seedling of some monocots. [APWeb:Glossary]

Currently part_of embryo, but it is also part of the seedling. It develops in the embryo, but persists after germination to protect the embryonic root. The coleorhiza, like the coleoptile, has an epidermis (and root hairs), and thus should be classified as a plant organ, even though many authors casually refer to it as a tissue.

Proposed definition: A plant organ that surrounds the radicle in the embryo and seedling.

Comment: Found in Poaceae and some other monocots. Protects the emerging embryonic root. The parenchyma cells of both the coleorhiza and epiblast may function in storage.

New children:

embryonic coleorhiza (PO:0025288): A coleorhiza that is part of a plant embryo.

seedling coleorhiza (PO:0025289): A coleorhiza that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic coleorhiza


  • hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]

currently is_a cardinal organ part, propose is_a stem internode (we didn't have this term before but do now)

Proposed definition: A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.

is_a stem internode

New children:

embryonic hypocotyl (PO:0025290): A hypocotyl that is part of a plant embryo.

seedling hypocotyl (PO:0025291): A hypocotyl that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic hypocotyl

Some discussion of hypocotyl hook or apical hook. We already have the term PO:0000012 (apical hook, synonym hypocotyl hook), part_of hypocotyl.


  • hypocotyl-root junction (PO:0004724): A cardinal organ part that is the part of a plant axis where a radicle joins a hypocotyl.

Moved to is_a cardinal organ part.

Proposed definition: A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.

synonym: embryo axis transition zone (Bell and Bryan 2008, and others)

New children:

embryonic hypocotyl-root junction (PO:0025300): A hypocotyl-root junction that is part of an embryo axis.

seedling hypocotyl-root junction (PO:0025301): A hypocotyl-root junction that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic hypocotyl-root junction

Add Poaceae crown as narrow synonym of hypocotyl-root junction.


  • epicotyl (PO:0020035): The first internode of a stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. [APWeb:Glossary]

currently is_a embryonic plant structure, propose is_a stem internode (PO:0005005). Also, the second part of the current definition only adds ambiguity. Need to define it more precisely.

Proposed definition: The first stem internode above a hypocotyl. [Esau]

Comment: The epicotyl is the first internode of a stem above the cotyledons.

New children:

embryonic epicotyl (PO:0025292): A epicotyl that is part of a plant embryo.

seedling epicotyl (PO:0025293): A epicotyl that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic epicotyl


  • mesocotyl (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.

This definition sounds like the same thing as an epicotyl. Esau says the mesocotyl is the plant axis between the scutellum and the coleoptile and that in grasses, the scutellum is generally thought to represent the cotyledon and the coleoptile to represent the first leaf. In that case, the mesocotyl (as the axis between the scutellum and the coleoptile), is analogous (or homologous) to the epicotyl in dicots and other monocots. In grasses, the hypocotyl is not visible, except perhaps as the scutellar node.

For a picture, see http://www.agry.purdue.edu/ext/corn/news/timeless/GerminationEvents.html

Proposed definition: A shoot internode that is the part of an embryo axis or the stem of a seedling above the scutellum and below the coleoptile. [Easu]

Comment: Occurs in grasses. In grasses, the hypocotyl and cotyledon may not be visible and may be represented by the scutellar node and scutellum, making the mesocotyl similar to the epicotyl in other taxa. Elongation of the mesocotyl during seedling growth pushes the coleoptile above the soil surface.

New children:

embryonic mesocotyl (PO:0025294): A mesocotyl that is part of a plant embryo.

seedling mesocotyl (PO:0025295): A mesocotyl that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic mesocotyl


  • embryonic root (PO:0000045): A root that is initiated in a developing embryo. [TAIR:ki]

Embryonic root is not part_of embryo (at present). Has children radicle (PO:0020031) and seminal root (PO:0000046).

Will need to revisit this when we look at organization of root (PO:0009005)


  • radicle (PO:0020031): The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive. is_a embryonic root [APWeb:Glossary]

Proposed definition: An embryonic root that is the basal continuation of a hypocotyl in an embryo.

Comment: May develop into the root system of an adult plant. Sometimes abortive.

Primary root (PO:0020127) develops from radicle.

New children:

embryonic radicle (PO:0025296): A radicle that is part of a plant embryo.

seedling radicle (PO:0025297): A radicle that is part of a whole plant in the seedling phase.

(can't add participates in seedling phase yet) develops_from embryonic radicle


Except as noted above, the above definitions were accepted. Will reword the definitions of all of the seedling terms to reflect that they develop from the embryonic structures and post on Source Forge

New terms for Physcomitrella and related taxa (continued)

Collective plant structures:

gametophore (PO:0030018)

Definition supplied by Moss Ontology: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Suggest is_a shoot system.

Proposed def.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.

participates_in gametophytic phase, develops_from gametophore bud

Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.

subset for bryophytes

Accepted

gametophore bud (PO:0030026)

The term "bud" has been requested: Def'n supplied by Moss Ontology: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A vegetative bud that develops into a gametophore.

Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.

participates_in gametophytic phase, has_part gametophore apical cell

synonym: brown bud

Accepted

thallus (PO:0030027)

From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.

From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.


Saying a thallus is a gametophore implies that it is a shoot system and therefore a collective plant structure (CPS). As a CPS, it must have more that one organ. This is not true for a thallus (sometime they branch, so you could say they have multiple axes, but it is a stretch. Maybe better to classify it as a whole plant.


proposed def: A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.

Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.


Add prothallium as a broad synonym of thallus and as a narrow synonym of whole plant.

Accepted

Other gametophyte terms

We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.

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.


We already have the term apical cell (PO:0004000), which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." The embryonic apical cell can also be found in non-angiosperms. Suggest obsoleting PO:0004000 and replacing it with the new term embryonic apical cell for clarity, and using the name apical cell for the general class of apical cells described below.


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 the apical cell can give rise to more than two cells (because it can have three or four cutting faces).


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 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. Will review definition at next meeting.


Suggested ontology structure for the children of apical cell:

Apical cell1.jpg

The dotted lines represent relations inferred by the reasoner.

Includes two ways of classifying: 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.

This ontology structure was approved.

During the meeting PJ posted this link in the chat: SAM Review

New terms and definitions for apical cells

Definitions for the descendents of apical cell were approved, pending approval of final definition of apical cell.

gametophytic apical cell (PO:0030014): An apical cell that is part of a whole plant in the gametophytic phase.

Comment: Occurs bryophytes and pteridophytes.

intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase


sporophytic apical cell (PO:0030015): An apical cell that is part of a whole plant in the sporophytic phase.

Comment: Occurs in pteridophytes and the sporophyte of bryophytes.

intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase


thallus apical cell (PO:0030025): An apical cell that is part of a thallus.

part_of thallus


root apical cell (PO:0030008): A sporophytic apical cell that is part of a root apical meristem.

comment: Occurs in the sporophytic phase of pteridophytes.

part_of root apical meristem


shoot apical cell (PO:0030009): An apical cell that is part of a shoot system.

comment: May occur in shoot axes or leaves of bryophytes or ferns.

part_of shoot system


gametophore apical cell (PO:0030019): A shoot apical cell that is part of a gametophore.

comment: Occurs in the non-vascular shoot system of the gametophyte of mosses and leafy liverworts.

intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore


leaf apical cell (PO:0030011): A shoot apical cell that is part of a leaf apex.

comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some ferns. Only in plants where leaf growth is apical.

part_of leaf apex


non-vascular leaf apical cell (PO:0030013): A leaf apical cell that is part of a leaf apex of a non-vascular leaf.

comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.

part_of non-vasucular leaf; synonym: phyllid apical cell


vascular leaf apical cell (PO:0030012): A leaf apical cell that is part of the leaf apex of a vascular leaf.

comment: Occurs in vascular leaves of some ferns in their sporophytic phase.

part_of vascular leaf


shoot axis apical cell (PO:0030010): An apical cell at the tip of a shoot apical meristem.

Comment: Divides to produces leaf initial cells (if leaves are present) and other stem or branch tissues.

part_of shoot apical meristem


gametophore axis apical cell (PO:0030023): A shoot axis apical cell at the tip of a gametophore axis.

Comment: Occurs at the tips of the stems and branches of bryophytes.

part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell


vascular shoot axis apical cell (PO:0030024): A shoot axis apical cell at the tip of a shoot apical meristem in a shoot system that has as part vascular tissue.

Comment: Occurs in some ferns in their sporophytic phase.

participates_in sporophytic phase; synonym: fern shoot axis apical cell


seta apical cell (PO:0030016): A shoot axis apical cell at the tip of a seta.

Comment: Ceases being an apical cell when the sporangium begins to develop.

part_of seta

Also:

embryonic apical cell (PO:0025284, replaces PO:0004000): An apical cell that is part of a plant embryo and is the uppermost cell formed after the first division of a zygote.

Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain meristematic throughout the plant's life.

Review for OBO Foundry Acceptance

At last weeks meeting, BS suggested that the PO can be submitted for OBO Foundry membership within the next weeks

By email after the call: BS sent us a link to the list of principles: [OBO_Foundry_Principles] and then CM sent:"Use the list here": [Accepted]

Which one is the one to use?

Upcoming meetings 2011:

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

Next meeting scheduled for Thur, April 28th, 2011 at 10am PDT

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