POC Conf. Call 12-1-10

POC meeting, Webex Conference Call; Date: Wednesday Dec 1st, 2010 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the POC Conf. Call 11-17-10?

Top Level PSO structure -- anatomical spaces, portion of plant substance, plant anatomical entity

Pores and anatomical space (Approval of changes from 11-5)

New top level term (sibling to plant structure) called plant anatomical space. This term would be parent to pore and slit. This would allow us to add new terms for slits or fissures as they come up.

Suggested definitions:

plant anatomical space: An anatomical space (CARO:0000005) that is part of a plant.

Ref. anatomical space (CARO:0000005): Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

Children of plant anatomical space:

• pore (PO:0025118): A plant anatomical space that is roughly circular and forms an opening in a plant structure.

• slitNew term,

proposed def'n: A plant anatomical space that is roughly linear and forms an opening in a plant structure.

This will allow us to create is_a parents for the following terms:

• micropyle (PO:0020025): "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]

comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. subset: reference

Suggested def: A pore that forms an opening in the integuments at the apex of an ovule. part_of integument. Comment: The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated.

• seed micropyle (PO:0006334): "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]

relationship: develops_from PO:0020025 micropyle; part_of seed coat

Current definition is okay

• stomatal pore (PO:0008032): "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]

synonym: "stomatal aperture" RELATED; relationship: part_of PO:0002000 stomatal complex

Suggested def'n: A pore in an epidermis, flanked by two guard cells. Comment: The size of the stomatal pore is variable and controlled by movement of the guard cells in response to environmental cues. part_of stomatal complex

• floral stomatal pore (PO:0008046): "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt] relationship: part_of PO:0008044 ! floral stomatal complex

Proposed def'n: A stomatal pore that is part of a floral stomatal complex. part_of floral stomatal complex

• stomium (PO:0020101): "A fissure or pore in the anther lobe through which the pollen is released."

[GR:pj] subset: reference, relationship: part_of PO:0005011 ! anther dehiscence zone

Proposed def'n: A slit in an anther lobe formed from when a dehiscence zone dehisces. Comment: Pollen may be released through the stomium. part_of anther

• anther pore (requested by TraitNet)

Proposed def'n: A pore at the apex of an anther. Comment: Pollen may be released through the anther pore. part_of anther

Plant body substance/portion of plant substance

Last week, we discussed adding a new upper level term for plant body substances. Perhaps a more consistent name would be portion of plant substance.

Possible children: Latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, sporopollenin.

We can add the upper level term now, but suggest waiting to populate it, as this is not a priority for this release.

Suggested definition: plant body substance: A portion of organism substance that is or was part of a plant.

Ref.: portion of organism substance (CARO:0000004): Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.

Anatomical entity

At the 11-10-10 meeting, Barry suggested that we have only two branches in the ontology (one for independent continuants and one for occurants). Should we make a new top level term plant anatomical entity, which would be parent to plant structure, plant anatomical space, and portion of plant substance (see below)? See dev browser for proposed structure.

Suggested def: An anatomical entity that is or was part of a plant. [source: CARO:0000000]. Comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces.

Continuation of older agenda items

Primordium, approval of changes from 10-5-10

At the POC meeting on 11-5-2010, we agreed to add the new term primordium, child of portion of plant tissue.

Proposed def: A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure.

There was some discussion of whether or not we should keep the comment "A visible primordium of an organ is the first distinct stage of the respective organ development.

Have deleted is_a relations between primordia and the structures they develop into and replaced with develops_from relations (e.g., leaf develops from leaf primordium).

Although we have the term adventitious root primordium, can’t add adventitious root develops form adventitious root primordium, b/c adventitious root is a synonym for several terms.

Also added new term: phyllome primordium, which is parent to leaf primordium, petal primordium, etc.

Parts of root tip (continued from meeting on 10-26-10)

Proposed new parent term: root parenchyma (PO:0025095): A portion of parenchyma tissue that is part of a root system.

root cap: PO:0020123

original def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary], subset: reference

Suggest: is_a root parenchyma

Proposed definition: A portion of root parenchyma tissue that is part of the root tip and covers the root apical meristem. Comment: Often composed of living and dead parenchyma cells. Protects the root apical meristem.

central root cap: PO:0020130

original def: "The central part of a root cap in which the cells are arranged in longitudinal files." [GR:pj], synonym: "columella cells" RELATED [] plus columella root cap, relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma

Proposed definition: A portion of root parenchyma tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.

lateral root cap: PO:0020131

original def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704], synonym: "peripheral cells" RELATED [], relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma

Proposed definition: A portion of parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis. comment: This is the general term for the lateral portion of any root cap and not the term for a root cap of lateral root (PO:0003018) or lateral root cap of lateral root (PO:0003020).

quiescent center: PO:0020149

original def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]

Suggest: is_a meristem, part_of root apical meristem

Proposed definition: A hemispherically shaped portion of meristem tissue consisting of mitotically and metabolically inactive cells that is part of the root apical meristem and is positioned behind the root cap.

differentiation zone: PO:0020135, alt_id: PO:0003002

original def: "The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function." [GR:pj], subset: reference, synonym: "maturation zone" RELATED [], synonym: "specialization zone" RELATED []

Suggest: is_a cardinal organ part, part_of root

Proposed new name: root differentiation zone; Proposed definition: A cardinal organ part that is the part of a root and is located behind the elongation zone and contains cells that are differentiating into their final form and function.

Comment: Most of the primary tissues of a root mature in the differentiation zone. This zone is where root hairs are produced.

Could add new parent term "shoot axis differentiation zone" to be parent to this term and to stem internode differentiation zone (PO:0008042)

elongation zone: PO:0020125

original def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj], subset: reference, synonym: "region of cell elongation" RELATED [], synonym: "region of radial enlargement" RELATED []

Suggest: obsoleting this term, because the definition is wrong, and making a new term, root elongation zone; is_a cardinal organ part, part_of root tip

Proposed definition: A cardinal organ part that is part of a root that is located directly behind a root apical meristem, in which the cells are undergoing longitudinal expansion.

Comment: The elongation zone is only a few millimeters in length and is the only portion of the root in which cell elongation generally occurs. Root hairs are not yet produced in this region. Primary root tissue begin to differentiate in the root elongation zone.

Could add new parent term "shoot axis elongation zone" to be parent to this term and to stem internode elongation zone (PO:0008041)