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)]==
 +
 
 +
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: [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]==
 +
 
 +
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
 +
 
 +
'''[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
 +
 
 +
 
 +
*'''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.''
 +
 
 +
 
 +
*'''[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
 +
 
 +
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:
 +
 
 +
[[File: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.''
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3132600&group_id=76834&atid=835555 Sporangium]==
 
  
−
We currently have the class '''sporangium''' (PO:0025094), which is a cardinal organ part.  
+
*'''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]
  
−
'''Current def:''' A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]
+
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.
  
−
Comment: May be multicellular or unicellular. In bryophytes, particularly in mosses, a sporangium is referred to as a capsule
+
'''Proposed definition:''' The first stem internode above a hypocotyl. [Esau]
  
−
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.
+
Comment: The epicotyl is the first internode of a stem above the cotyledons.
  
 +
'''New children:'''
  
−
'''Proposed definition:''' A plant organ in which spores are produced.
+
'''embryonic epicotyl (PO:0025292)''': A epicotyl that is part of a plant embryo.
  
−
Comment: May be multicellular or unicellular. 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.
+
'''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
  
−
We also have:
 
  
−
'''megasporangium''' (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]
+
*'''mesocotyl''' (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.
  
−
'''microsporangium''' (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]
+
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.
  
−
'''nucellus''' (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]
+
For a picture, see http://www.agry.purdue.edu/ext/corn/news/timeless/GerminationEvents.html
  
−
Comment: In seed plants, the megaspores and megagametophyte are retained within the nucellus.
+
'''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]
  
−
'''pollen sac''' (PO:0025277): A microsporangium that is part of a sporophyll where the pollen grains developed and are contained after they develop. [source: POC:curators]
+
Comment: 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: 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.
+
'''New children:'''
  
 +
'''embryonic mesocotyl (PO:0025294)''': A mesocotyl that is part of a plant embryo.
  
−
'''Proposed def. nucellus:''' A megasporangium in a seed plant, composed of fleshy subepidermal tissue ''located in'' an ovule and surrounding a megasporocyte.  
+
'''seedling mesocotyl (PO:0025295)''': A mesocotyl that is part of a whole plant in the seedling phase.
  
−
'''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]
+
(can't add participates in seedling phase yet) develops_from embryonic mesocotyl
  
−
(comments stay the same)
 
  
−
We could continue to use the more general part_of relation for located_in, if we don't want to add a new relation.
+
*'''embryonic root''' (PO:0000045): A root that is initiated in a developing embryo. [TAIR:ki]
  
−
==Sporangium parts==
+
Embryonic root is not part_of embryo (at present). Has children '''radicle''' (PO:0020031) and '''seminal root''' (PO:0000046).
  
−
This is continued from our discussion at the [[POC_Conf._Call_3-8-11]]
+
Will need to revisit this when we look at organization of root (PO:0009005)
  
−
Currently classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002). However, these layers and their constituent cell types can be part of any sporangium, not just an anther. Proposed making them part of a general class sporangium wall (as we did for parts of leaf).
 
  
−
From Smith, Cryptogramic Botany:
+
*'''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]
  
−
Liverworts: Embryo divides to form outer layer (ampithecium) that gives rise to jacket layer and inner mass (endothecium) that gives rise to archesporium (cells of which divide to produce sporocytes and nurse cell, may also produce elators).
+
'''Proposed definition:''' An embryonic root that is the basal continuation of a hypocotyl in an embryo.
  
−
Hornworts: Embryo divides to form ampithecium that gives rise to jacket layer and primiary sporogenous layer, and endothecium that gives rise to sterile columella in all but one species (where it gives rise to sporagenous tissue). Jacket layer is 4-6 cells thick, and outer layer develops into epidermis. Sporagenous tissue gives rise to sporocytes and filaments of sterile cells called pseudoelators.
+
Comment: May develop into the root system of an adult plant. Sometimes abortive.
  
−
Sphagnum: Upper tier of cells in the embryo divides to form endothecium that gives rise to sterile columella and ampithecium that gives rise to outer sterile layer and inner archesporium. Archesporium gives rise to sporogenous layer two to four cells thick. Outer sterile layer gives rise to jacket layer 3 or 4 cells thick.
+
Primary root (PO:0020127) develops from radicle.
  
−
Eubrya: Early division of capsule gives rise to multilayered ampithecium and endothecium (with ampithecial cells and endothecial cells). Endothecium (usually) gives rise to archesporium and columella. Columella cells adjacent to archesporium remain small and develop into inner spore sac. Ampithecium develops into a multilayered structure, including layers with and without chloroplasts and an epidermis.
+
'''New children:'''
  
−
Psilophyta: Paired sporangia (a synangium or maybe a reduced sporangiophore) develop from a single cell. First cell division leads to a jacket initial and an archesporial (primary sporogenous) cell. Repeated periclinal divisions of jacket initial lead to jacket layer four or five cells thick and divisions of archesporial cell lead to many sporogenous cells. No tapetum develops. Near maturity, irregular clumps of sporogenous tissue divide to give rise to spore mother cells, remainder disintegrate
+
'''embryonic radicle (PO:0025296)''': A radicle that is part of a plant embryo.
  
−
Lycopods: Sporangia borne on sporophylls. Early cell division leads to a layer of jacket initials and an archesporium, which divides to form a mass of sporogenous tissue. Nearly all cells in this tissue function as spore mother cells that divide to for tetrads of megaspores. Tapetum is formed from innermost layer of jacket cells and outer layer of sporogenous tissue. Unlike most pteridophytes, tapetum does not break down during sporogenesis.
+
'''seedling radicle (PO:0025297)''': A radicle that is part of a whole plant in the seedling phase.
  
−
Selaginellaceae: Has microsporanigia and megasporangia borne on microsporophylls and megasporophylls that are always in strobili (maybe in same or different strobili). Development of mega- and microsporangia is the same up to sporocyte stage. One or multiple cells divide to form outer jacket initial(s) and inner archesporial cell(s). Inner cells develop into mass of sporogenous tissue while outer develop into jacket layer two cells thick, outer layer with thick-walled cells and inner layer with thin-walled cells. A distinct tapetum develops from the outer layer of sporogenous cells.
+
(can't add participates in seedling phase yet) develops_from embryonic radicle
  
−
Isoetaceae: Each sporophyll bears a single flattened sporangia between the ligule and the leaf base, which is covered by a membranous outrgrowth from the epidermis just below the ligule called a '''velum''. Early development of mega- and microsporangia is similar. Several cells divide to form jacket jacket initials and archesporial cells. Archesporial cells divide to form mass of sporogenous tissue. Later in development, this is divided into blocks of fertile cells divided by sterile cells. The sterile cells mature into trabeculae, that incompletely divide the sporangium chamber. Sporogenous cells adjacent to trabeculae and jacket layers form a tapetum that is generally two cells thick. Remaining sporogenous cells may become sporocytes. Jacket layer may become 3 or 4 cells thick.
 
  
−
Equisetum and allies: Sporangia are borne on branching sporangiophores and are associated with sterile bracts. Sporangiophores are clustered on the plant axis alternating with bracts (in extinct taxa), but it is not strictly correct to call it a strobilus, since it is not composed of sporophylls. Fossil taxa are a mix of hetero- and homosporous species. Equisetum has strobili with clusters of sporangiophores. Sporangia are of the eusporangiate type in that they are not entirely derived from a single initial cell, but all of the sporogenous tissue can be traced to s single cell. First cell division gives rise to inner cell that will give rise to the sporogenous tissue and outer cell that gives rise to part of the jacket layer, the remainder coming from cells lateral to original cell. Jacket layer is several cells thick, with inner layer functioning as tapetum. Tapetum and inner jacket layers disintegrate during development. Disintegrated SMCs and tapetum and jacekt cells form a liquid in which spores float. Spores form an outer exosporium that splits into four strips called '''elaters'''.
+
''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''
  
−
Ferns: Sporangia may be borne on the margin of a leaf blade, or on the abaxial surface. May be scattered over the surface or grouped in clusters ('''sorus'''). The sori may be covered by an '''indusium'''. In eusporangiate ferns, sori may be borne on a specialized part of the leaf blade ('''fertile spike''')
+
=New terms for Physcomitrella and related taxa (continued)=
  
−
Two types of sporangium development:  
+
==Collective plant structures:==
  
−
Leptosporangiate ferns: Sporangia develop from a single initial cell.  
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore (PO:0030018)]===
  
−
Eusporangiate ferns: Sporangia develop from more than one initial cell. Each sporangium contains an indefinite large number of spores and has a jacket layer more than one cell thick.  
+
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.
  
−
Ophioglossales: The fertile spike grows from a pyramidal apical cell which produces four quadrants of cells. Strips of epidermal cells (2 to 3 cells wide and several cells tall) on the two quadrants that are perpendicular to the leaf blade develop into '''sporangiogenic bands''' which then become three or 4 cells thick. The band differentiates into blocks of sterile cells and archesporial cells. Each block of archesporial cells divides to form a large number of sporogenous cell. The cells in the band external to the archesporium divide periclinally to form a jacket layer, and the cells between the sporangia also divide. Each sporangium becomes surrounded by a poorly defined tapetum which may come from the outer sporogenous cells or the inner sterile cells (unknown). Tapetum breaks down inot plasmodial mass with persistent nuclei in between SMCs.
+
Suggest is_a shoot system.
  
−
Marattitales:
+
'''Proposed def.:''' A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.
  
−
==Plant Cells==
+
participates_in gametophytic phase, develops_from gametophore bud
  
−
Terms requested by MO:
+
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.
  
−
===archesporial cell===
+
subset for bryophytes
  
−
We have the terms:
+
''Accepted''
  
−
'''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]  
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud (PO:0030026)]===
  
−
'''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]
+
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.
  
−
Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.
+
Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
  
−
Proposed definitions:
+
participates_in gametophytic phase, has_part gametophore apical cell
  
−
'''archesporial cell''' A plant cell that gives rise to a sporocyte.
+
synonym: brown bud
  
−
Comment: May be part of an archesporium.
+
''Accepted''
  
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus (PO:0030027)]===
  
−
'''female archesporial cell''' (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.
+
From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.
  
−
Comment: Found in heterosporous ferns and seed plants. 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]
+
From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.
−
 
  
−
'''male archesporial cell''' (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.
 
  
−
Comment: Male archesporial cell may undergo periclinal division, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
+
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.
  
−
===alar cell===
 
  
−
===brachycyte===
+
'''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
  
−
chloronema cell - done
+
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.
  
−
caulonema cell - done
 
  
−
===tmema cell===
+
Add '''prothallium''' as a broad synonym of thallus and as a narrow synonym of whole plant.
  
−
===jacket layer cell===
+
''Accepted''
  
−
===axillary hair terminal cell===
+
===Other gametophyte terms===
  
−
===axillary hair base cell===
+
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.
  
−
===neck canal cell===
+
==[https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 apical cell]==
  
−
===side branch initial===
+
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'''.
  
  
−
===Other cell types, not requested by MO:===
+
Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.
  
−
hyrdoid
 
  
−
leptoid
+
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.
  
−
rhizoid initial
 
  
−
==Plant Tissues==
+
'''Definition of apical cell from Esau:''' The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
  
−
===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)
+
'''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.
  
−
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."
+
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).  
  
−
Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
 
  
−
Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.
+
'''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.
  
−
'''Proposed definition:''' A plant organ/portion of plant tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.
+
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.
  
−
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.
+
-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
  
−
[[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
+
''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.''
  
  
−
===midrib/costa===
+
Suggested ontology structure for the children of apical cell:
−
Moss Ontology definition: The nerve of a phyllid. Altered from Bill and Nancy Malcolm (2006)
 
  
−
We have term midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary] (which, by the way, should just say phyllome, instead of leaf or leaf-like organ). However, midvein is_a leaf vein, which is a portion of vascular tissue, so it cannot apply to mosses.
+
[[File:apical_cell1.jpg]]
  
−
We should have a term that groups conductive tissue together for both vascular and non-vascular plants, kind of like we have axial cell for vascular and non-vascular conductive cells.
+
The dotted lines represent relations inferred by the reasoner.
  
−
New child of portion of plant tissue: portion of axial tissue:  
+
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.''
  
−
(also, we need to redefine phloem to be more like definition of xylem, and not based on function)
+
''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]
−
(need to redefine axial cell so it doesn't say vascular cell)
 
  
−
===rhizoid===
+
===New terms and definitions for apical cells===
  
−
archesporium
+
''Definitions for the descendents of apical cell were approved, pending approval of final definition of apical cell.''
  
−
amphithecium
+
'''gametophytic apical cell (PO:0030014):''' An apical cell that is part of a whole plant in the gametophytic phase.
  
−
endothecium
+
Comment: Occurs bryophytes and pteridophytes.
  
−
jacket layer
+
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
  
−
paraphysis
 
  
−
axilliary hair
+
'''sporophytic apical cell (PO:0030015):''' An apical cell that is part of a whole plant in the sporophytic phase.
  
−
tmema
+
Comment: Occurs in pteridophytes and the sporophyte of bryophytes.
  
−
=Continuing User requests: for PSO=
+
intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase
  
−
- Deal with and complete the list of user requests on SourceForge-
 
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]==
+
'''thallus apical cell (PO:0030025):''' An apical cell that is part of a thallus.  
  
−
submitted by Austin Mast
+
part_of thallus
  
−
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
 
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165981&group_id=76834&atid=835555 fascicle] The term fascicle can refer to different structures in different taxa. Suggest we use the term '''floral fascicle''' or '''flower fascicle''' in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
+
'''root apical cell (PO:0030008)''': A sporophytic apical cell that is part of a root apical meristem.
  
−
From Tucker, 2003, Flora:
+
comment: Occurs in the sporophytic phase of pteridophytes.
−
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
 
−
that two to several flowers are initiated in each bract axil rather than
 
−
just one as in a raceme. '''The cluster of flowers at each node is called a fascicle.''' The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows
 
−
'''the fascicle to be a short shoot topped by a second order inflorescence apical meristem'''. This meristem initiates
 
−
flowers in a bilaterally symmetrical order: a single abaxial flower, then
 
−
two lateral flowers, another median abaxial, then two more laterals. The
 
−
number of flowers per fascicle depends on the duration of the axillary
 
−
inflorescence apex of the short shoot, which ceases activity after
 
−
initiating the few flowers in the fascicle. No flowers are initiated
 
−
adaxially (toward the first order axis) on the short shoot (Tucker, 1987b;
 
−
Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be
 
−
distinguished from a cyme in that every flower is bract subtended in a
 
−
pseudoraceme."
 
  
−
'''Proppsed def:''' A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated.  Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
+
part_of root apical meristem
  
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle] (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
'''shoot apical cell (PO:0030009)''': An apical cell that is part of a shoot system.
  
−
We added the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
+
comment: May occur in shoot axes or leaves of bryophytes or ferns.
  
−
Alternative is to suggest bristled to PATO
+
part_of shoot system
  
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]
+
'''gametophore apical cell (PO:0030019)''': A shoot apical cell that is part of a gametophore.
  
−
'''Proppsed def:''' A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
+
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
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]
 
  
−
'''Banner''' (as in a legume flower) - suggest using name 'banner petal'
+
'''leaf apical cell (PO:0030011)''': A shoot apical cell that is part of a leaf apex.
  
−
'''Proppsed def:''' A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
+
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
  
−
'''Wing''' (as in a legume flower) - suggest using name 'wing petal'
 
  
−
'''Proppsed def:''' One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.
+
'''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.
  
−
'''Keel''' (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name 'corolla keel'
+
part_of non-vasucular leaf; synonym: phyllid apical cell
  
−
Suggest three new terms:
 
  
−
'''fused petal:''' A petal that is fused to another petal.  
+
'''vascular leaf apical cell (PO:0030012)''': A leaf apical cell that is part of the leaf apex of a vascular leaf.
  
−
Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
+
comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
  
 +
part_of vascular leaf
  
−
'''fused corolla:''' A corolla in which the petals are fused.
 
  
−
Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
+
'''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.
  
−
'''corolla keel:''' A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae.
+
part_of shoot apical meristem
  
−
Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
 
  
−
==TraitNet requests==
+
'''gametophore axis apical cell (PO:0030023)''': A shoot axis apical cell at the tip of a gametophore axis.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]
+
Comment: Occurs at the tips of the stems and branches of bryophytes.
  
−
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
+
part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
  
−
child of stem (PO:0009047).
 
  
 +
'''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.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]
+
Comment: Occurs in some ferns in their sporophytic phase.
  
−
Their comment: is synonym to Tubercle
+
participates_in sporophytic phase; synonym: fern shoot axis apical cell
  
−
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
 
  
−
tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
+
'''seta apical cell (PO:0030016)''': A shoot axis apical cell at the tip of a seta.
  
−
proposed def:
+
Comment: Ceases being an apical cell when the sporangium begins to develop.
  
 +
part_of seta
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
+
Also:
  
−
definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
+
'''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.
  
−
proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
+
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
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]
+
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]]
  
−
definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
+
Which one is the one to use?
  
−
We could add this term as a kind of upper level bin term (similar to trichome)
+
=Upcoming meetings 2011:=
  
 +
'''[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.
 +
'''
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.  
  
−
Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
+
-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.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]
+
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
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from Crum (2001): a cluster of fern sporangia
 
−
from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
 
  
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Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
+
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
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Part_of vascular leaf, has_part sporangium
+
[http://icbo.buffalo.edu 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.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
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'''Full-Day Workshops Schedule:'''
  
−
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
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'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
tendrils can derived from multiple types of structures. Suggest we make separate terms:
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
−
leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
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leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
+
- LC will attend and represent the PO. Invite other plant people?
  
−
leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
 
  
−
Can add other types of tendrils if they come up or users need them.
 
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
submitted by Rich Zobel (Nov 2009)
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
−
=User requests still open on Source Forge; PGDSO =
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
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==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]==
 
  
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This item has been open on SF since 6/2009
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
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I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
+
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
  
−
Suggested stages:
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
 
  
−
-tuber initiation
 
  
−
-tuber growth
+
'''* International Botanical Congress (IBC2011)'''
  
−
-tuber maturation
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
How we work these in will depend on restructuring of PGDSO
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
+
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.  
  
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==[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed development stages]==
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.  
  
−
This is a fairly new request for terms for cotton
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
−
=Next meeting scheduled for Tues, May 3rd, 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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