POC Conf. Call 4-12-11
POC meeting, Webex Conference Call; Date: Tuesday April 12th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_4-5-11?
Items arising from last week's meeting:
embryo
embryo (PO:0009009) current definition: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.
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.
This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.
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.
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.
Could add zygotic and haploid embryo as children of embryo
Should talk to Melissa Haendel about how they handle haploid and diploid embryos in Zebrafish.
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.
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.
embryonic plant structures
Tabled till next week
Definition of embryonic plant structure:
embryonic plant structure (PO:0025099): A plant structure that is part of an embryo.
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.
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:
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.
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
Both now have cross-product definitions, and no asserted is_a children
embryonic plant cell (PO:0025028): A plant cell that is part of an embryo.
is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
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)
Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.
(portion of) embryonic plant tissue (PO:0025233): A portion of plant tissue that is part of an embryo.
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo
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.
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.
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.
Here is a picture of some plant tissues, to show how it works:
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?
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.
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]
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 definition: A root that is initiated in a developing embryo.
radicle (PO:0020031): The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive. is_a embryonic root [APWeb:Glossary]
Proposed definition: An embryonic root that is the basal continuation of a hypocotyl in an embryo and may develop into the root system of an adult plant.
Comment: Sometimes abortive.
remove part_of embryo axis.
hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]
currently is_a cardinal organ part, propose is_a stem internode (we didn't have this term before but do now)
Proposed definition: A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.
is_a stem internode
epicotyl (PO:0020035): The first internode of a stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. [APWeb:Glossary]
currently is_a embryonic plant structure, propose is_a stem internode (PO:0005005). Also, the second part of the current definition only adds ambiguity. Need to define it more precisely.
Proposed definition: The first stem internode above a hypocotyl.
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?
made is_a stem internode
hypocotyl-root junction PO:0004724: A cardinal organ part that is the part of an embryonic axis where the radicle joins the hypocotyl.
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.
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.
made is_a terminal bud, part_of embryo
scutellar node (PO:0004708): The region in of an embryo axis between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached. [MaizeGDB:lv]
Sounds like it should be is_a stem node.
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).
is_a stem node, part_of embryo axis
Cardinal organ parts
Terms requested by MO:
Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.
We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named perianth calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.
Proposed name and def.: spore capsule calyptra: A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.
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.
participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?
subsets for bryophytes, pteridophytes
[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77
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
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
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
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
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.
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
part_of peristome
subsets for bryophytes
- Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.
We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.
Proposed name and def.: spore capsule operculum: A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
Comment: Found in mosses. May remain partly attached to the rest of the capsule.
Synonym: sporangium lid
part_of sporangium
subsets for bryophytes
Also add these terms for angiosperms:
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. part_of fruit
The top part of the bud where the perianth (petals) is fused. Leaves fruit underneath it. Operculum is underneath that
Comment: Found in Eucalyptus.
Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
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.
Comment: Found in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit.
Proposed definition: A plant anatomical space that is the opening on the apical end of a spore capsule.
Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
part_of sporangium
subsets for bryophytes
Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
Proposed definition: A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.
Comment: Present in some moss species of the family Polytrichaceae.
Synonym: tympanum, epiphram
subsets for bryophytes
From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
Proposed definition: A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
participates_in gametophytic phase
subsets for bryophytes
