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

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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:=
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 embryo]==
+
==[https://sourceforge.net/tracker/?func=detail&aid=2932524&group_id=76834&atid=835555 plant cell]:(PO:0009002)==
  
−
embryo (PO:0009009) '''current definition:''' A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.
+
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: 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.
+
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]
  
−
This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.
+
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 definition:''' A whole plant in the sporophytic phase that is contained in an archegonium or a seed.
+
-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.
  
−
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]''
  
−
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.
+
''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
  
−
''Could add zygotic and haploid embryo as children of embryo''
+
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.
  
−
''Should talk to Melissa Haendel about how they handle haploid and diploid embryos in Zebrafish.''
+
''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.''
  
−
''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.''
+
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2944945&group_id=76834&atid=835555 portion of plant tissue] (PO:0009007)==
  
−
''Discussion of haploid embryos. Are they still in the sporophytic phase? ''
+
'''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]
−
''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.''
+
Comment: These cells are organized into a structural unit, and may include an intercellular matrix.
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]==
+
There are several problems with this definition:
  
−
''Tabled till next week''
+
-It does not exclude cardinal organ parts.
  
−
===Definition of embryonic plant structure:===
+
-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).
  
−
'''embryonic plant structure''' (PO:0025099): A plant structure that is part of an embryo.
+
Also: it is not consistent with our definition of plant structure which is "an anatomical structure that '''is or was''' part of a plant."
  
−
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.
+
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."
  
−
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.
 
  
−
===Some terms were left as is_a children of embryonic plant structure:===
+
'''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.
  
−
'''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.
+
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.
  
−
'''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.
+
''There was an extensive discussion about this class and how to include the requisite features and also differentiate it from the cardinal organ part.''
  
−
'''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===
+
''new proposed def'n: A multicellular plant structure which consists predominantly of similarly specialized cells of one or more types.''
−
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.
+
-Should add disjoint_from cardinal organ part.
  
−
is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
+
-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
  
−
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
 
  
−
Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)
+
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.
  
−
Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, 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.
  
−
'''(portion of) embryonic plant tissue''' (PO:0025233): A portion of plant tissue that is part of an embryo.
+
Proposed new def’n: A plant structure that is grown or maintained ''in vitro''.
  
−
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo
+
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''.
  
−
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.
+
''All were in favor of the proposed definition and comment. Accepted and closed''
  
−
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.
 
  
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3279819&group_id=76834&atid=835555 cultured protoplast]'''(PO:0000006):
  
 +
Current Def’n: In vitro isolated cells from which the entire cell wall has been enzymatically removed.
  
−
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.
+
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
  
−
Here is a picture of some plant tissues, to show how it works:
 
  
−
[[File:Embryonic plant structure.jpg]]
+
Comment: The cell wall is generally removed using polysaccharide-degrading enzymes such as cellulase, pectinase and /or xylanase.
  
−
===Proposed changes/questions for structures that were is_a embryonic plant structure:===
+
Note: The cultured plant cell may be in suspension culture or from callus culture on solid media
  
−
'''embryonic leaf''' (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].
+
''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.''
  
−
Is this an embryonic plant structure, that is, is it always part of the embryo?
+
''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]''
  
−
'''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.
+
''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.''
  
−
is_a vascular leaf, part_of embryo (need to confirm part_of relation)
 
  
  
−
'''embryonic root''' (PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]
+
'''* [https://sourceforge.net/tracker/?func=detail&aid=3280004&group_id=76834&atid=835555 callus]  (PO:0005052)'''
  
−
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.
+
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]
  
−
'''Proposed definition:''' A root that is initiated in a developing embryo.
+
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]]
  
−
'''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]
+
''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 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.
+
''Proposed new def'n: A portion of plant tissue that consists of mass of undifferentiated plant cells''
  
−
Comment: Sometimes abortive.
 
  
−
remove part_of embryo axis.
+
'''* 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.
  
−
'''hypocotyl''' (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]
+
Comment: None
  
−
currently is_a cardinal organ part, propose is_a stem internode (we didn't have this term before but do now)
+
cultured callus (PO:0000009):  (Rename cultured plant callus?) yes
  
−
'''Proposed definition:''' A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.
+
Proposed def’n: An ''in vitro'' plant structure consisting of a mass of undifferentiated plant cells.
  
−
is_a stem internode
+
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
  
−
'''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 new def’n: A plant callus grown or maintained in vitro.''
  
−
'''Proposed definition:''' The first stem internode above a hypocotyl.
+
''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.''
  
−
'''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. Should they be synonyms?
+
== ''Tabled for discussion at the next meeting, please see: [[POC_Conf._Call_4-14-11]] for details'' ==
  
−
made is_a stem internode
+
===Cultured cells===
  
 +
'''* cultured cell''' (PO:0000005):
  
−
'''hypocotyl-root junction''' PO:0004724: A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.
+
'''* cultured root cell (PO:0000008): Proposed new name: root-derived cultured plant cell'''
  
−
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.
+
'''* cultured leaf cell (PO:0000007); Proposed new name: leaf-derived cultured plant cell:'''
  
 +
===Cultured embryos===
  
−
'''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.
+
'''*cultured plant embryo (PO:0000010):'''
  
−
made is_a terminal bud, part_of embryo
+
'''*cultured somatic embryo: (PO:0000011):'''  Child of cultured plant embryo
  
 +
===Removing the part_of relationships to [https://sourceforge.net/tracker/index.php?func=detail&aid=2968335&group_id=76834&atid=835555 whole plant]?===
  
−
'''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]
+
===[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo (PO:0009009)]===
  
−
Sounds like it should be is_a stem node.
+
===[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]===
  
−
'''Proposed definition:''' A stem node that is the part of an embryo axis where the scutellum is attached.
 
  
−
Comment: A scutellum is attached to an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile).
+
===Children of embryonic plant structure:===
  
−
is_a stem node, part_of embryo axis
+
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.
  
−
=New terms for Physcomitrella and related taxa (continued)=
+
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.
  
−
==Cardinal organ parts==
+
scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
−
Terms requested by MO:
 
  
−
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234979&group_id=76834&atid=835555 calyptra]'''
+
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.
  
−
Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.
+
===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.
  
−
We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named '''perianth calyptra''' (see below under operculum), and this term should be named '''spore capsule calyptra''', to distinguish them.
+
apical cell (PO:0004000)  
  
−
'''Proposed name and def.: spore capsule calyptra:''' A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.
+
basal cell (PO:0002002)
  
−
Comment: Found in bryophytes and pteridophytes (''according to Parihar''). The calyptra ia a membranous or hairy cap or hood composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.
+
hypophysis (PO:0020109)
  
−
participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?
+
(portion of) embryonic plant tissue(PO:0025233): A portion of plant tissue that is part of an embryo.
  
−
subsets for bryophytes, pteridophytes
+
New inferred children of embryonic plant tissue:
  
−
[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77
+
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:===
  
−
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234981&group_id=76834&atid=835555 venter]''' 
+
embryonic leaf (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].
−
 
 
−
This term was not suggested by Moss Ontology, but perhaps we should add it.
 
−
 
 
−
'''proposed def.:''' A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.
 
−
 
 
−
part_of archegonium
 
−
 
 
−
subsets for bryophytes, pteridophytes, gymnosperms
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3234985&group_id=76834&atid=835555 archegonium neck]'''
 
−
 
 
−
This term was not suggested by Moss Ontology, but perhaps we should add it.
 
−
 
 
−
'''proposed def.:''' A cardinal organ part that is the elongated apica part of an archegonium.
 
−
 
 
−
Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.
 
−
 
 
−
part_of archegonium
 
−
 
 
−
(can also add term for neck canal cell when we deal with cells)
 
−
 
 
−
subsets for bryophytes, pteridophytes, gymnosperms
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241725&group_id=76834&atid=835555 base]'''
 
−
 
 
−
'''Proposed name and def.: sporangium base''': A cardinal organ part that is the basal part of a sporangium.
 
−
 
 
−
Comment:  Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)
 
−
 
 
−
part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
 
−
 
 
−
subsets for bryophytes
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241737&group_id=76834&atid=835555 theca]'''
 
−
 
 
−
Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 
−
 
 
−
We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that '''anther theca''' and call this term '''sporangium theca:'''.
 
−
 
 
−
'''Proposed name and def.: sporangium theca:''' A cardinal organ part that is the main body of a sporangium and has spores located in it.
 
−
 
 
−
Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
 
−
 
 
−
part_of sporangium
 
−
 
 
−
subsets for bryophytes, maybe pteridophytes
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241747&group_id=76834&atid=835555 peristome]'''
 
−
 
 
−
Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 
−
 
 
−
'''proposed definition:''' A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.
 
−
 
 
−
Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.
 
−
 
 
−
part_of sporangium
 
−
 
 
−
subsets for bryophytes
 
−
 
 
−
 
 
−
*'''peristome tooth'''
 
−
 
 
−
Not requested by Moss Ontology, but should add it.
 
  
−
'''Proposed def:''' A cardinal organ part that is a single lobe or tooth of a peristome.
+
embryonic root(PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]
  
−
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
+
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.
  
−
part_of peristome
+
hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]
  
−
subsets for bryophytes
+
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.
  
−
*Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
+
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.
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241767&group_id=76834&atid=835555 lid/operculum]'''
+
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]
  
−
Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.
+
==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]]
  
−
We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.
+
Action taken:
 +
-LC talked with CM, we all agreed that it would not be too much of an issue to do so.
  
−
'''Proposed name and def.: spore capsule operculum:''' A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
+
-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"
  
−
Comment: Found in mosses. May remain partly attached to the rest of the capsule.
+
-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.
  
−
Synonym: sporangium lid
+
-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?
  
−
part_of sporangium
+
=Upcoming meetings 2011:=
  
−
subsets for bryophytes
+
'''[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.
 +
'''
  
−
===Also add these terms for angiosperms:===
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
  
−
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 fruit operculum]:''' A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. apical part of a circumsesile fruit.
+
-JE and JP will be attending
−
part_of fruit
 
  
−
The top part of the bud where the perianth (petals) is fused. Leaves fruit underneath it. Operculum is underneath that
+
-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 Eucalyptus.
+
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
−
Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
 
  
−
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 perianth calyptra]:''' A collective plant structures that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.
+
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
−
Comment: Found in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit.
+
[http://icbo.buffalo.edu ICBO]
  
−
==Other related terms for mosses, not from Moss Ontology==
+
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.
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241816&group_id=76834&atid=835555 spore capsule mouth]'''
+
'''Full-Day Workshops Schedule:'''
  
−
'''Proposed definition:''' A plant anatomical space that is the opening on the apical end of a spore capsule.
+
'''July 26 9am-6pm''' The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
part_of sporangium
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
−
subsets for bryophytes
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
 +
- LC will attend and represent the PO.  Invite other plant people?
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241820&group_id=76834&atid=835555 epiphragm]'''
 
  
−
Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
 
  
−
From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
'''Proposed definition:''' A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.  
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
−
Comment: Present in some moss species of the family Polytrichaceae.
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
−
Synonym: tympanum, epiphram
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
−
subsets for bryophytes
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241827&group_id=76834&atid=835555 pseudopodium]'''
 
  
−
From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
+
'''* International Botanical Congress (IBC2011)'''
  
−
From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
'''Proposed definition:''' A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
−
Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
+
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.  
  
−
participates_in gametophytic phase
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
  
−
subsets for bryophytes
+
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"