POC Conf. Call 6-19-12
POC meeting, Webex Conference Call; Date: Tuesday June 19th, 2012 10am PDT/1pm EDT
In attendance:
POC members:
Absent:
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_6-12-12?
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New upper level terms for Plant Anatomical Entity branch of the PO
under construction
New proposed hierarchy:
need to update the figure
Collective plant structure (new term) should be a subtype of plant structure. Some discussion of whether or not CPS's are "distinct structural units". Probably not all are, so better to keep under plant structure
New proposed term: multi-tissue plant structure (MTPS) (PO:0025496)
proposed def., MTPS: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single, distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
This is derived from the CARO term: multi-tissue structure (CARO:0000055): Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component.
We decided last week that CPS (and its children CPOS and CPOP) should not be subtypes of MTPS, because they are not always distinct structural units.
We discussed the difference between bona-fide and fiat boundaries. Bona-fide boundaries include things like the boundary between epidermis and air or between two tissue types. Fiat boundaries are more or less arbitrary, such as the boundary between a hand and wrist. In reality, organs are not completely separated by bona fide boundaries, but are often connected to other organs by pipe-like structures.
Sub-classes of MTPS:
plant organ (PO:0009008):
current def.: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.
comment: Examples: stem, leaf, root. May include individual cell types that are not part of tissues (e.g.: idioblasts).
new proposed def'n: plant organ (PO:0009008): A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
new proposed comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts (PO:0000283)). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an plant ovule (PO:0020003).
seed (PO:0009010):
Current def'n: A plant structure that develops from an ovule and has as parts an embryo enclosed in a seed coat.
propose revised def'n: A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).
fruit (PO:0009001)
proposed def.: A multi-tissue plant structure (PO:0025496) containing one or more plant embryos (PO:0009009), which as a whole, develops from a gynoecium (PO:0009062).
comment: A fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions. Fruits only occur in angiosperms.
New term: collective plant structure (PO:0025497)
This would be a general term, parent to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269); see below. The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts).
proposed definition: A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008), or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
Sub-classes of collective plant structure (PO:)
collective plant organ structure (PO:0025007)
This is currently named collective plant structure. At the POC meeting on 5-?-12, we discussed renaming it "collective plant organ structure", which is clearer.
Changed name, and slight change to clarify that the two organs must be adjacent, not one part_of the other. Otherwise, a sporophyll would be a collective plant organ structure.
New proposed def.: A collective plant structure (PO:PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacentplant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
comment: A collective plant organ structure must have as parts at least two plant organs (PO:0009008) that do not have a part_of relation between them, that is, one must be adjacent to the other, rather than one part of the other. The plant organs in a collective plant structure can be of the same type, such as the corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006), composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.
collective organ part structure (PO:0025269)
This is the existing term that is currently defined as: "A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue." examples are septum, pseudostem etc.
propose revised def'n: A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) from adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).
comment stays as is
Sub-classes for the parts of the various multi-tissue plant structures
These are subclasses of plant structure, not of multi-tissue plant structure, since they do not necessarily for "distinct structural units" (although some, like leaflet, do).
cardinal part of multi-tissue plant structure (PO:0025498)
This is similar to "cardinal plant organ" (or cardinal part of plant organ) but includes parts of multi-tissue plant structures that are not organs (e.g., aril, which is part of seed).
Proposed def.: A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types.
Comment: Includes cardinal parts of plant organs as well as other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary, including parts with both fiat boundaries, such as leaf base (PO:id), and bona-fide boundaries, such as leaflet (PO:id).
cardinal organ part (PO:0025001)
current def'n: A plant structure that is a proper part of an organ and includes portions of tissues of at least two different types.
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include lobe (PO TBD), operculum (PO TBD), neck (PO TBD), petiole PO:0020038, leaflet PO:0020049.
Do we want to rename this cardinal part of plant organ?
proposed new def.: A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
revised comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.
Re': fiat versus bona-fide boundaries:
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.
This is what we call a cardinal part.
BS: Biological significance is not all of the story for cardinal parts. They should also have their own boundaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.
CARO has terms for "organism subdivision", which includes things like appendages that are separated by fiat boundaries, and "multi-tissue structure", which includes things like organs that are separated by bona-fide boundaries. However, it does not appear to have any terms of for organ parts.
We need to check with CARO to found out how they plan to deal with organ parts.
FMA has the following hierarchy for organ parts (definitions paraphrased):
anatomical structure
>cardinal organ part: any part of an organ that has two or more tissues
>>organ component: a cardinal organ part which is bounded predominantly by bonafide boundaries
>>organ region: a cardinal organ part which is a fiat subdivision of an organ (includes organ segments and organ zones)
>>region of organ component: a cardinal organ part which is a fiat subdivision of an organ component. (RW: This seems redundant with organ region to me)
plant ovary (PO:0009072):
current def'n: A plant structure that is the basal portion of a carpel or group of fused carpels and encloses the ovule(s).
note: An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc
Cardinal part of MTPS does not work as a parent for this, because it does not have a bona-fide boundary. Still have the issue that ovary can be part of either carpel (a plant organ/MTPS) or gyneocium (a CPOS).
