Difference between revisions of "POC Conf. Call 4-12-11"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(142 intermediate revisions by 2 users not shown)
Line 3: Line 3:
 
In attendance:  
 
In attendance:  
  
−
POC members:   
+
POC members:  Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Barry Smith (University at Buffalo, NY)
  
−
Absent:
+
Absent: Dennis Stevenson (NYBG), Justin Elser (OSU), Chris Mungall (Lawrence Berkeley National Lab), Justin Preece (OSU)
  
−
Collaborators:  
+
Collaborators: none
  
  
−
Acceptance of the minutes from the [[POC_Conf._Call_4-5-11]]?
+
Acceptance of the minutes from the [[POC_Conf._Call_4-5-11]]? ''There were no changes additions or deletions.''
  
  
 
=Items arising from last week's meeting:=
 
=Items arising from last week's meeting:=
  
−
==in vitro plant structures==
+
==[https://sourceforge.net/tracker/?func=detail&aid=2932524&group_id=76834&atid=835555 plant cell]:(PO:0009002)==
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 embryo]==
+
Current def’n:  A cell that is part of a plant and that has as its parts a plant cell wall. [source: GO:0005623, ISBN:0471245208, POC:curators]  
  
−
embryo (PO:0009009) '''current definition:''' A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.
+
Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid). Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". See definition of plant-type cell wall GO:0009505. Egg and sperm cells lack the cell wall.
  
−
Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.
+
'''Proposed def’n:''' An anatomical structure that is or was part of a plant and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding cell wall. [source: POC:curators, GO:0005623]
  
 +
Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid). Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". See definition of plant-type cell wall GO:0009505.  Egg and sperm cells lack the cell wall.
  
−
This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.
+
-By using 'plant structure' we cover any cells are are or were parts of a plant, plus it makes it in the g-d format.
  
−
'''Proposed definition:''' A whole plant in the sporophytic phase that is contained in an archegonium or a seed.
 
  
−
Comment: The embryo is a whole plant after fertilization (post-zygotic) and before emergence from the archegonium (for bryophytes and pteridophytes) or seed germination (for seed plants). Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures.
+
''Proposed new def’n: A cell which is a plant structure. [source: POC:curators, GO:0005623]''
  
 +
''Add to the comment: Includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. ''
  
−
Logically, an embryo could be treated like a sporophyte or gametophyte, that is, as a cross-product of whole plant and the appropriate life cycle phase. However, since we don't have embryonic phase yet, and since so much research is done on embryos, it may be appropriate to keep the class embryo, and pre-compose the cross-product once we have embryonic phase.
+
'''plant-type cell wall:''' GO:0009505  exact: cellulose and pectin-containing cell wall
  
 +
Def'n: A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.
  
−
''Could add zygotic and haploid embryo as children of embryo''
+
''There was an extensive discussion about how to define the plant cell and we decided to continue the use of the GO term "cell" as the genus term, and add the differentia, "which is a plant structure".  We looked at the GO def'n of plant type cell wall to ensure it was not introducing circularity. We agreed to remove" Egg and sperm cells lack the cell wall." from the comment.  This definition should work well for cultured cells, as well.''
  
−
''Should talk to Melissa Haendel about how they handle haploid and diploid embryos in Zebrafish.''
+
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2944945&group_id=76834&atid=835555 portion of plant tissue] (PO:0009007)==
  
−
''If we want cultured plant embryo to be a child of embryo, we will need to remove the comment here that they are in vitro plant structures.''
+
'''current definition:''' A plant structure that has as its parts multiple cells and is a proper part of an organ. [source: POC:curators, TAIR:lr]  
−
 
 
−
''Discussion of haploid embryos. Are they still in the sporophytic phase? ''
 
−
''RW: Yes, because they develop into haploid sporophytes, even if those sporophytes may be sterile. This happens naturally in many ferns and sometimes in bryophytes (apogamy - when a gametophyte gives rise to a sporophyte without syngamy). The reverse also happens (apospory -- when a sporophyte gives rise to a gametophyte without meiosis).''
 
−
 
 
−
''LC: Note: Haploid embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.''
 
−
 
 
−
==portion of plant tissue (PO:0009007)==
 
−
 
 
−
current definition: A plant structure that has as its parts multiple cells and is a proper part of an organ. [source: POC:curators, TAIR:lr]  
 
  
 
Comment: These cells are organized into a structural unit, and may include an intercellular matrix.
 
Comment: These cells are organized into a structural unit, and may include an intercellular matrix.
Line 55: Line 48:
 
-It does not exclude cardinal organ parts.
 
-It does not exclude cardinal organ parts.
  
−
-Saying that it is a proper part of an organ does not work for cultured callus of for tissues in plants that don't have any organs (like a protonema or thallus).
+
-Saying that it is a proper part of an organ does not work for cultured callus or for tissues in plants that don't have any organs (like a protonema or thallus).
−
 
 
  
−
Proposed definition:
+
Also: it is not consistent with our definition of plant structure which is "an anatomical structure that '''is or was''' part of a plant."
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]==
+
From FMA: "...consists predominantly of similarly specialized cells, with or without cells of other types and intercellular matrix"
  
−
''Tabled till next week''
+
From CARO:0000043 (also used by TAO): "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships."
  
−
===Definition of embryonic plant structure:===
 
  
−
'''embryonic plant structure''' (PO:0025099): A plant structure that is part of an embryo.
+
'''Proposed definition:''' A plant anatomical structure that has as its parts multiple cells of the same type(s) aggregated according to genetically determined spatial relationships.
  
−
Comment: Includes organs, tissues and cell types that are unique to embryos, not plant structures that can occur in both embryos and mature plant structures.
+
Comment: A portion of plant tissue may contain one or several types of cells. These cells are organized into a structural unit and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts in parenchyma tissue.
  
  
−
Changed definition from "proper part of" to "part of", so it would be consistent with the intersection of term. Think part_of is better anyway, because technically an embryo is an embryonic plant structure.
+
''There was an extensive discussion about this class and how to include the requisite features and also differentiate it from the cardinal organ part.''
  
−
===Some terms were left as is_a children of embryonic plant structure:===
 
  
−
'''coleoptile''' (PO:0020033): A tubular embryonic structure developed at the junction of the cotyledonary sheath with the seedling axis, and surrounding the plumule of a monocot embryo or seedling.
+
''new proposed def'n: A multicellular plant structure which consists predominantly of similarly specialized cells of one or more types.''
  
−
'''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.
+
-Should add disjoint_from cardinal organ part.
  
−
'''scutellum''' (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
+
-Need to remove the part_of whole plant relation, so we can include '''cultured callus''' (see below).
  
−
'''suspensor''' (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.
+
==''In vitro'' plant structures==
 +
We agreed last week that the ''in vitro'' structures should be children of their respective plant structure parents (cell, tissue, and embryo). This required a little revision on some of the terms (see below). Also, removed part_of relationships to whole plant between plant cell and portion of plant tissue.- redundant
  
−
===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 an embryo.
+
After much searching and discussion with developers of the other ontologies (details are available, but don't want to take up the whole meeting with them), we decided it was better to just keep "in vitro plant structure" and use a textual definition and assert dual parentage to it. This was after consultation with PATO, OBI, and GO, specifically CM.
  
−
is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
+
'''* [https://sourceforge.net/tracker/?func=detail&aid=2958948&group_id=76834&atid=835555''in vitro'' plant structure]'''(PO:0000004):
  
 +
Current definition:  A plant structure that was derived from part of a plant and involves microbe-free growth in a sterile environment.
  
−
Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion
+
Proposed new def’n: A plant structure that is grown or maintained ''in vitro''.
  
−
Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)
+
Comment: ''In vitro'' growth is defined as microbe-free growth in a sterile, culture environment, usually in the laboratory.
 +
An example of a sterile culture environment is growth on or in a nutrient medium in a Petri dish, culture flask or test tube. Microbes may be intentionally added to the culture environment, such as in co-culture with ''Agrobacterium''.
  
−
Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.
+
''All were in favor of the proposed definition and comment. Accepted and closed''
  
  
−
'''(portion of) embryonic plant tissue''' (PO:0025233): A portion of plant tissue that is part of an embryo.
+
*'''[https://sourceforge.net/tracker/?func=detail&aid=3279819&group_id=76834&atid=835555 cultured protoplast]'''(PO:0000006):
  
−
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo
+
Current Def’n: In vitro isolated cells from which the entire cell wall has been enzymatically removed.
  
−
coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (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 embryonic plant tissue.
+
Propose renaming:''' plant protoplast''' (PO:0000006) ('cultured' is redundant here)
  
−
This is a little odd, because we define embryo (PO:0009009) as: "A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues," but I guess there is nothing in the definition of epidermis or cortex, etc, that says that they are fully differentiated. May want to put a comment under embryonic tissue to that effect.
+
Proposed def’n: A cultured plant cell from which the entire plant cell wall has been removed.
 +
 +
-is_a cultured plant cell, (based on the revised plant cell definition above), and is_a in vitro plant structure
  
  
 +
Comment: The cell wall is generally removed using polysaccharide-degrading enzymes such as cellulase, pectinase and /or xylanase. 
  
−
Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.
+
Note: The cultured plant cell may be in suspension culture or from callus culture on solid media
  
 +
''We discussed whether or not it made sense to have two terms "cultured plant protoplast" and "plant protoplast" to differentiate protoplasts that were maintained for long periods of time in culture, but we decided that this probably was covered by the definition as written.  Plus, it would be difficult to distinguish between them on a temporal basis (ie: at what point does one become the other?).  Maybe could add "cultured plant protoplast" later as needed.''
  
−
Here is a picture of some plant tissues, to show how it works:
+
''PJ supplied a couple of citations as evidence of longer term culture of plant protoplasts for our reference:
 +
[http://pcp.oxfordjournals.org/content/31/7/999.abstract Cultured Equisetum protoplasts] and [http://pcp.oxfordjournals.org/content/31/7/999.abstract Kaur et al, 2006]''
  
−
[[File:Embryonic plant structure.jpg]]
+
''Comment from DWS on SF: "Ok. I just wanted to be sure that we do not want to include gametes. I do (not) know for sure but I do not think sperm have a plasmalemma. Eggs do have a plasmalemma and cytoplasm. However, for plants the notion of naturally occurring makes sense to me.''
  
−
===Proposed changes/questions for structures that were is_a embryonic plant structure:===
 
  
−
'''embryonic leaf''' (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].
 
  
−
Is this an embryonic plant structure, that is, is it always part of the embryo?  
+
'''* [https://sourceforge.net/tracker/?func=detail&aid=3280004&group_id=76834&atid=835555 callus]  (PO:0005052)'''
  
−
'''Proposed definition:''' A vascular leaf that is one of the first few leaves to develop from the embryonic shoot apical meristem and is part of an embryo.
+
We need to revise the definition of this term as it currently covers the cultured callus as well.
 +
Current definition: A tissue formed as a result of wounding, or a tissue developing in a tissue culture. [source: GR:pj]
  
−
is_a vascular leaf, part_of embryo (need to confirm part_of relation)
+
parentage: >> parenchyma >> portion of ground tissue >> portion of plant tissue
  
 +
We discussed this on last weeks POC conference call 4-5-11 [[POC_Conf._Call_4-5-11]]
  
−
'''embryonic root''' (PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]
+
''Renamed "plant callus".  Discussed the proposed new definition should refer to the generic case of the callus and the "cultured plant callus" should be a child of it.  Will make it only a child of "is_a portion of plant tissue", rather than specifying parenchymatous tissue''
  
−
Propose that this should be is_a root instead of is_a embryonic plant structure, b/c it is not necessarily part of an embryo.
+
''Proposed new def'n: A portion of plant tissue that consists of mass of undifferentiated plant cells''
  
−
'''Proposed definition:''' A root that is initiated in a developing embryo.
 
  
 +
'''* cultured plant callus (PO:0000009):'''
  
−
'''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]
+
Current Def’n: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium supplemented by plant growth regulators.
  
−
'''Proposed definition:''' An embryonic root that is the basal continuation of a hypocotyl in an embryo and may develop into the root system of an adult plant.
+
Comment: None
  
−
Comment: Sometimes abortive.
+
cultured callus (PO:0000009):  (Rename cultured plant callus?) yes
  
−
remove part_of embryo axis.
+
Proposed def’n: An ''in vitro'' plant structure consisting of a mass of undifferentiated plant cells.
  
 +
Comment: Cultured callus may originate from isolated protoplasts, cell suspensions or from callus that was induced in sterile medium supplemented by plant growth regulators. Plant cell calluses may be made to differentiate into the specialized tissues of a whole plant, with the addition of a number of hormones or enzymes.
  
−
'''hypocotyl''' (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]
+
has_part cultured plant cells, is_a  in_vitro plant structure
  
−
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.
+
''Proposed new def’n: A plant callus grown or maintained in vitro.''
  
−
is_a stem internode
+
''is_a plant callus,  is_a  in_vitro plant structure, has_part cultured plant cells''
  
 +
'' proposed slightly modified existing comment:''
 +
''Cultured plant callus may induced to form from plant protoplasts or cultured plant cells in suspension culture.  After supplementation with the appropriate plant growth regulators, further differentiation may lead to the development of plant tissues and ultimately a whole plant.''
  
−
'''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.
+
== ''Tabled for discussion at the next meeting, please see: [[POC_Conf._Call_4-14-11]] for details'' ==
  
−
'''Proposed definition:''' The first stem internode above a hypocotyl.
+
===Cultured cells===
  
 +
'''* cultured cell''' (PO:0000005):
  
−
'''mesocotyl''' (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.
+
'''* cultured root cell (PO:0000008): Proposed new name: root-derived cultured plant cell'''
  
−
This definition sounds like the same thing as an epicotyl. Should they be synonyms?
+
'''* cultured leaf cell (PO:0000007); Proposed new name: leaf-derived cultured plant cell:'''
  
−
made is_a stem internode
+
===Cultured embryos===
  
 +
'''*cultured plant embryo (PO:0000010):'''
  
−
'''hypocotyl-root junction''' PO:0004724: A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.
+
'''*cultured somatic embryo: (PO:0000011):''' Child of cultured plant embryo
  
−
Moved to is_a cardinal organ part. Will automatically be is_a embryonic plant structure b/c it is part of embryonic axis. Is this accurate? The hypocotyl-root junction remains after germination.
+
===Removing the part_of relationships to [https://sourceforge.net/tracker/index.php?func=detail&aid=2968335&group_id=76834&atid=835555 whole plant]?===
  
 +
===[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo (PO:0009009)]===
  
−
'''plumule'''(PO:0020032): A somewhat differentiated terminal bud in several embryo types above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.
+
===[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]===
  
−
made is_a terminal bud, part_of embryo
 
  
 +
===Children of embryonic plant structure:===
  
−
'''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]
+
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.
  
−
Sounds like it should be is_a stem node.
+
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.
  
−
'''Proposed definition:''' A stem node that is the part of an embryo axis where the scutellum is attached.
+
scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
  
−
Comment: A scutellum is attached to an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile).
+
suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.
  
−
is_a stem node, part_of embryo axis
+
===New definitions for embryonic plant cells and tissues===
 +
'''[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 an embryo.
  
−
=New Physcomitrella and related terms=
+
apical cell (PO:0004000)
−
==Collective plant structures:==
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3244685&group_id=76834&atid=835555 vascular and non-vascular shoot systems]===
 
  
−
The Moss Ontology did not request these terms, but suggest adding them in order to classify shoot systems.
+
basal cell (PO:0002002)
  
−
'''non-vascular shoot system:''' A shoot system that does not have as part vascular tissue.
+
hypophysis (PO:0020109)
  
−
comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.
+
(portion of) embryonic plant tissue(PO:0025233): A portion of plant tissue that is part of an embryo.
  
−
subsets for bryophytes
+
New inferred children of embryonic plant tissue:
  
 +
coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049)
  
−
Could we use the relation "lacks_part"? Then we could define this class using intersection_of relations, which would be better. CL has used this (lack_plasma_membrane_part). Works better in OWL; translates into something like has_part exactly 0 (some Y).
+
===Proposed changes/questions for structures that were is_a embryonic plant structure:===
−
 
 
−
 
 
−
Child of non-vascular shoot system will be gametophore (see below). A moss sprophyte could also be called a non-vascular shoot system. If we used the lacks_part relation and intersection_of relations, we could make gameotophore a child of shoot system, and the reasoner would infer it was a non-vascular shoot system.
 
−
 
 
−
Can't use participates_in gametophytic phase, because the sporophyte of a bryphyte doesn't have roots or vascular tissue.
 
−
 
 
−
 
 
−
 
 
−
'''vascular shoot system:'''  A shoot system that has as part vascular tissue.
 
−
 
 
−
comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
 
−
 
 
−
participates_in sporophytic phase, has_part vascular system
 
−
 
 
−
 
 
−
If we accept these terms, suggest changing definitions of '''vascular leaf''' (PO:0009025) and '''non-vascular leaf''' (PO:0025075) to "A leaf that is part of a vascular/non-vascular shoot system.  This would be better than the current definitions which reference their taxonomy (part of a vascular or non-vascular plant) and would help with reasoning.
 
−
 
 
−
'''root-bourne shoot system''' (PO:0004544) should be is_a vascular shoot system
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore]===
 
−
 
 
−
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 non-vascular 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
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud]===
 
−
 
 
−
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 bud that develops into a gametophore.
 
−
 
 
−
Comment: Occurs in mosses and leaf liverworts. Develops from a caulonema cell in mosses.
 
−
 
 
−
participates_in gametophytic phase, has_part gametophore apical cell
 
−
 
 
−
synonym: brown bud
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus]===
 
−
 
 
−
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 always 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.
 
−
 
 
−
===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.
 
−
 
 
−
==[https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 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:''' 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 is established upon the first cell division of an embryo or germination of a spore.
 
−
 
 
−
-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
 
−
 
 
−
 
 
−
Suggested ontology structure for the children of apical cell:
 
−
 
 
−
[[File: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.
 
−
 
 
−
 
 
−
===New terms and definitions for apical cells===
 
−
 
 
−
 
 
−
'''gametophytic apical cell:''' An apical cell that is part of a whole plant in the gametophytic phase.
 
−
 
 
−
Comment: Occurs in mosses and other bryophytes.
 
−
 
 
−
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
 
−
 
 
−
 
 
−
'''sporophytic apical cell:''' 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''': An apical cell that is part of a thallus.
 
−
 
 
−
part_of thallus
 
−
 
 
−
 
 
−
'''root apical cell''': A sporophytic apical cell that is part of a root apical meristem.
 
−
 
 
−
comment: Only occurs in the sporophytic phase of vascular plants.
 
−
 
 
−
part_of root apical meristem
 
−
 
 
−
 
 
−
'''shoot apical cell''': 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''': A shoot apical cell that is part of a gametophore.
 
−
 
 
−
comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.
 
−
 
 
−
intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
 
−
 
 
−
 
 
−
'''leaf apical cell''': 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 mosses. Only in plants where leaf growth is apical.
 
−
 
 
−
part_of leaf
 
−
 
 
−
 
 
−
'''non-vascular leaf apical cell''': 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''': 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:''' An apical cell at the tip of a shoot apical meristem.
 
−
 
 
−
Comment: Divides to produces leaf initial cells and other stem tissues.
 
−
 
 
−
part_of shoot apical meristem
 
−
 
 
−
 
 
−
'''gametophore axis apical cell''': 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''': A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.
 
−
 
 
−
Comment: Occurs in some ferns in their sporophytic phase.
 
−
 
 
−
part_of vascular_shoot system; synonym: fern shoot axis apical cell
 
−
 
 
−
 
 
−
Also:
 
−
 
 
−
'''embryonic apical cell (replaces PO:0004000)''':  An apical cell that is part of an embryo and is the uppermost cell formed after the first division of the 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.
 
−
 
 
−
==Plant organs:==
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]===
 
−
- This is the term used for the gametophore stem or axis.
 
−
 
 
−
Suggest using '''gametophore axis''' as primary name, cauloid as synonym.
 
−
 
 
−
'''Proposed def'n:''' A shoot axis that is part of a gametophore.
 
−
 
 
−
Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
 
−
 
 
−
intersection_of: is_a plant axis, intersection_of: part_of gametophore
 
  
−
Add caulome as synonym of shoot axis
+
embryonic leaf (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].
  
−
-Also suggest adding terms for '''gametophore stem''' and '''gametophore branch'''.
+
embryonic root(PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]
  
 +
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.
  
−
'''gametophore stem''': A stem that is part of a gametophore.
+
hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]
  
−
is_a stem, part_of gametophore
+
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]
−
 
  
−
'''gametophore branch''': A branch that is part of a gametophore.
+
mesocotyl (PO:0020037): The internode between the cotyledon or cotyledons and the leaf or leaves at the next node of a young sporophyte.
  
−
is_a branch, part_of gametophore
+
hypocotyl-root junction (PO:0004724): A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.
  
 +
plumule(PO:0020032): A somewhat differentiated terminal bud in several embryo types above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.
  
−
-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).
+
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]
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract]===
+
==Other items:==
 +
'''*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)'''
 +
This was discussed at the [[POC_Conf._Call_3-29-11]]
  
−
- The specialized phyllids surrounding the antheridia.  
+
Action taken:
 +
-LC talked with CM, we all agreed that it would not be too much of an issue to do so.
  
−
Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
+
-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"
  
−
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.
+
-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.
  
−
'''Proposed def'n:''' A bract that subtends an antheridium.
+
-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?
  
−
part_of gametophore, participates in gametophytic phase
+
=Upcoming meetings 2011:=
  
−
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.
+
'''[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=3234965&group_id=76834&atid=835555 foot]===
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.  
  
−
Moss Ontology definition: The base of the sporophytes in mosses
+
-JE and JP will be attending
  
−
'''Proposed name and def.: sporophyte foot:''' A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore. (ref: Schofeld)
+
-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.  
  
−
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)
+
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
−
participates_in sporophytic phase, has_part transfer cell, only_in_taxon bryophytes (I know this isn't a clade, will have to create a pseudo-clade).
 
  
−
==Additional organ related moss terms:==
+
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
−
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.
+
[http://icbo.buffalo.edu ICBO]
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perichaetal bract]===
+
LC is coorganizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
 +
along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
  
−
'''Proposed def'n:''' A bract that subtends an archegonium. part_of gametophore
+
'''Full-Day Workshops Schedule:'''
  
−
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.
+
'''July 26 9am-6pm''' The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth]===
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
'''Proposed def'n:'''  A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on a gametophore axis and surround the calyptra (capsule?).
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
−
Should it be surrounds the capsule, in case no calyptra is present?
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
−
-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)
+
- LC will attend and represent the PO.  Invite other plant people?
  
−
Comment: The parachaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
 
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185175&group_id=76834&atid=835555 seta]===
 
−
-The stalk of a moss sporophyte.
 
  
−
'''Proposed def.:''' A plant axis that that holds up a spore capsule. participates_in sporophytic phase
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
Comment: Found in some bryophytes, especially mosses.
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3272612&group_id=76834&atid=835555 antheridiophore and archegoniophore]===
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
−
These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
−
'''Proposed definitions:'''
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
−
'''antheridiophore:''' A plant axis that bears two or more antheridia.
 
  
−
participates_in gametophytic phase
 
  
−
Comment: Found in Marchantiales.
+
'''* International Botanical Congress (IBC2011)'''
  
−
'''archegoniophore:''' A plant axis that bears two or more archegonia.
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
participates_in gametophytic phase
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
−
Comment: Found in Marchantiales.
+
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.
  
−
Will also add terms for '''antheridium stalk''' and '''archegonium stalk''' for stalks that hold up a single antheridium or archegonium. part_of antheridium or archegonium
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
−
=Next meeting scheduled for Tues, Apr. 19th, 2011 at 10am PDT=
+
==Next meeting scheduled for Thursday, Apr. 14th, 2011 at 10am PDT==

Latest revision as of 00:57, 13 April 2011

POC meeting, Webex Conference Call; Date: Tuesday April 12th, 2011 10am (PDT)

In attendance:

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

Absent: Dennis Stevenson (NYBG), Justin Elser (OSU), Chris Mungall (Lawrence Berkeley National Lab), Justin Preece (OSU)

Collaborators: none


Acceptance of the minutes from the POC_Conf._Call_4-5-11? There were no changes additions or deletions.


Items arising from last week's meeting:

plant cell:(PO:0009002)

Current def’n: A cell that is part of a plant and that has as its parts a plant cell wall. [source: GO:0005623, ISBN:0471245208, POC:curators]

Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid). Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". See definition of plant-type cell wall GO:0009505. Egg and sperm cells lack the cell wall.

Proposed def’n: An anatomical structure that is or was part of a plant and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding cell wall. [source: POC:curators, GO:0005623]

Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid). Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". See definition of plant-type cell wall GO:0009505. Egg and sperm cells lack the cell wall.

-By using 'plant structure' we cover any cells are are or were parts of a plant, plus it makes it in the g-d format.


Proposed new def’n: A cell which is a plant structure. [source: POC:curators, GO:0005623]

Add to the comment: Includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall.

plant-type cell wall: GO:0009505 exact: cellulose and pectin-containing cell wall

Def'n: A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.

There was an extensive discussion about how to define the plant cell and we decided to continue the use of the GO term "cell" as the genus term, and add the differentia, "which is a plant structure". We looked at the GO def'n of plant type cell wall to ensure it was not introducing circularity. We agreed to remove" Egg and sperm cells lack the cell wall." from the comment. This definition should work well for cultured cells, as well.

portion of plant tissue (PO:0009007)

current definition: A plant structure that has as its parts multiple cells and is a proper part of an organ. [source: POC:curators, TAIR:lr]

Comment: These cells are organized into a structural unit, and may include an intercellular matrix.

There are several problems with this definition:

-It does not exclude cardinal organ parts.

-Saying that it is a proper part of an organ does not work for cultured callus or for tissues in plants that don't have any organs (like a protonema or thallus).

Also: it is not consistent with our definition of plant structure which is "an anatomical structure that is or was part of a plant."

From FMA: "...consists predominantly of similarly specialized cells, with or without cells of other types and intercellular matrix"

From CARO:0000043 (also used by TAO): "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships."


Proposed definition: A plant anatomical structure that has as its parts multiple cells of the same type(s) aggregated according to genetically determined spatial relationships.

Comment: A portion of plant tissue may contain one or several types of cells. These cells are organized into a structural unit and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts in parenchyma tissue.


There was an extensive discussion about this class and how to include the requisite features and also differentiate it from the cardinal organ part.


new proposed def'n: A multicellular plant structure which consists predominantly of similarly specialized cells of one or more types.

-Should add disjoint_from cardinal organ part.

-Need to remove the part_of whole plant relation, so we can include cultured callus (see below).

In vitro plant structures

We agreed last week that the in vitro structures should be children of their respective plant structure parents (cell, tissue, and embryo). This required a little revision on some of the terms (see below). Also, removed part_of relationships to whole plant between plant cell and portion of plant tissue.- redundant


After much searching and discussion with developers of the other ontologies (details are available, but don't want to take up the whole meeting with them), we decided it was better to just keep "in vitro plant structure" and use a textual definition and assert dual parentage to it. This was after consultation with PATO, OBI, and GO, specifically CM.

* in vitro plant structure(PO:0000004):

Current definition: A plant structure that was derived from part of a plant and involves microbe-free growth in a sterile environment.

Proposed new def’n: A plant structure that is grown or maintained in vitro.

Comment: In vitro growth is defined as microbe-free growth in a sterile, culture environment, usually in the laboratory. An example of a sterile culture environment is growth on or in a nutrient medium in a Petri dish, culture flask or test tube. Microbes may be intentionally added to the culture environment, such as in co-culture with Agrobacterium.

All were in favor of the proposed definition and comment. Accepted and closed


Current Def’n: In vitro isolated cells from which the entire cell wall has been enzymatically removed.

Propose renaming: plant protoplast (PO:0000006) ('cultured' is redundant here)

Proposed def’n: A cultured plant cell from which the entire plant cell wall has been removed.

-is_a cultured plant cell, (based on the revised plant cell definition above), and is_a in vitro plant structure


Comment: The cell wall is generally removed using polysaccharide-degrading enzymes such as cellulase, pectinase and /or xylanase.

Note: The cultured plant cell may be in suspension culture or from callus culture on solid media

We discussed whether or not it made sense to have two terms "cultured plant protoplast" and "plant protoplast" to differentiate protoplasts that were maintained for long periods of time in culture, but we decided that this probably was covered by the definition as written. Plus, it would be difficult to distinguish between them on a temporal basis (ie: at what point does one become the other?). Maybe could add "cultured plant protoplast" later as needed.

PJ supplied a couple of citations as evidence of longer term culture of plant protoplasts for our reference: Cultured Equisetum protoplasts and Kaur et al, 2006

Comment from DWS on SF: "Ok. I just wanted to be sure that we do not want to include gametes. I do (not) know for sure but I do not think sperm have a plasmalemma. Eggs do have a plasmalemma and cytoplasm. However, for plants the notion of naturally occurring makes sense to me.


* callus (PO:0005052)

We need to revise the definition of this term as it currently covers the cultured callus as well. Current definition: A tissue formed as a result of wounding, or a tissue developing in a tissue culture. [source: GR:pj]

parentage: >> parenchyma >> portion of ground tissue >> portion of plant tissue

We discussed this on last weeks POC conference call 4-5-11 POC_Conf._Call_4-5-11

Renamed "plant callus". Discussed the proposed new definition should refer to the generic case of the callus and the "cultured plant callus" should be a child of it. Will make it only a child of "is_a portion of plant tissue", rather than specifying parenchymatous tissue

Proposed new def'n: A portion of plant tissue that consists of mass of undifferentiated plant cells


* cultured plant callus (PO:0000009):

Current Def’n: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium supplemented by plant growth regulators.

Comment: None

cultured callus (PO:0000009): (Rename cultured plant callus?) yes

Proposed def’n: An in vitro plant structure consisting of a mass of undifferentiated plant cells.

Comment: Cultured callus may originate from isolated protoplasts, cell suspensions or from callus that was induced in sterile medium supplemented by plant growth regulators. Plant cell calluses may be made to differentiate into the specialized tissues of a whole plant, with the addition of a number of hormones or enzymes.

has_part cultured plant cells, is_a in_vitro plant structure


Proposed new def’n: A plant callus grown or maintained in vitro.

is_a plant callus, is_a in_vitro plant structure, has_part cultured plant cells

proposed slightly modified existing comment: Cultured plant callus may induced to form from plant protoplasts or cultured plant cells in suspension culture. After supplementation with the appropriate plant growth regulators, further differentiation may lead to the development of plant tissues and ultimately a whole plant.

Tabled for discussion at the next meeting, please see: POC_Conf._Call_4-14-11 for details

Cultured cells

* cultured cell (PO:0000005):

* cultured root cell (PO:0000008): Proposed new name: root-derived cultured plant cell

* cultured leaf cell (PO:0000007); Proposed new name: leaf-derived cultured plant cell:

Cultured embryos

*cultured plant embryo (PO:0000010):

*cultured somatic embryo: (PO:0000011): Child of cultured plant embryo

Removing the part_of relationships to whole plant?

plant embryo (PO:0009009)

embryonic plant structures

Children of embryonic plant structure:

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.

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 a basal cell and connects an embryo proper to the wall of a megagametophyte.

New definitions for embryonic plant cells and tissues

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

apical cell (PO:0004000)

basal cell (PO:0002002)

hypophysis (PO:0020109)

(portion of) embryonic plant tissue(PO:0025233): A portion of plant tissue that is part of an embryo.

New inferred children of embryonic plant tissue:

coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049)

Proposed changes/questions for structures that were is_a embryonic plant structure:

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

embryonic root(PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]

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.

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

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]

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

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

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

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]

Other items:

*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO) This was discussed at the POC_Conf._Call_3-29-11

Action taken: -LC talked with CM, we all agreed that it would not be too much of an issue to do so.

-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"

-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.

-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?

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 coorganizing 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.

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 Thursday, Apr. 14th, 2011 at 10am PDT

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-12-11&oldid=7395"