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:

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 of for tissues in plants that don't have any organs (like a protonema or thallus).

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 similarly specialized cells aggregated according to genetically determined spatial relationships and is a proper part of a plant.

Comment: These cells are organized into a structural unit and may include an intercellular matrix. May include other types of isolated cells, such as idoblasts in parenchyma tissue.

Should add disjoint_from cardinal organ part.

Do we want to include the part_of whole plant relation? This would exclude cultured callus.

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.

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.

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). Embryos that arise through apogamy, adventitious embryos, and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures.

Do we want to keep the comment that cultured embryos are in vitro plant structures?

Haploid embryos 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).

However, haploid embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization. Suggest that we rework the definition of sporophytic phase with a comment about apogamy.

We could add zygotic and haploid embryo as children of embryo.

gametophytic phase and sporophytic phase

sporophytic phase (PO:0028002)

Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.

Proposed definition: A plant life cycle phase (whole growth stage) that ...

gametophytic phase (PO:0028003)

Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]

Comment: During the gametophytic phase, a plant may produce gametes by mitosis.

Proposed definition: A plant life cycle phase (whole growth stage) that ...

embryonic plant structures

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.

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