POC Conf. Call 1-17-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 17th, 2012 10:30am (PST)

In attendance: POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-10-12?

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Term Requests from users

Vascular tissue:

from Agron-Omics.

freely ending veinlet: Part of leaf vein. Higher order veins that are only connected to other veins at one end.

proposed defintion: A leaf vein above the first order that is connected to another vein only at one end.

comment: May be branched or simple. Usually used with third order or higher veins. If vein order is known, an additional annotation should be place on secondary vein (PO:0020140), tertiary vein (PO:0008021), quaternary vein (PO:0008022), or higher order vein (PO:0008023).

Note: PO currently does not have a term for first order or primary vein, but we have this term requested under Items_for_future_meetings#leaf_vein.2C_midrib.2C_costa

pappus

From Shawna Thompson.

From FNA glossary: A set of one or more awns (aristae, bristles, setae) or scales at the summit of an inferior ovary just beneath or outside the free portion of the corolla; persisting in the fruit (cypsela) and often aiding wind or animal dispersal; in Asteraceae (Compositae). Considered by some to be an evolutionarily modified upper calyx portion, the lower portion having been incorporated into the floral tube casing adnate to the ovary wall; considered by others to be an outgrowth from the ovary wall.

From Harris and Harris: The modified calyx of the Asteraceae, consisting of awns, scales, or bristles at the apex of the achene.

proposed definition, pappus: A collective organ part structure that has a parts one or more pappus elements (scales, awns, or bristles) at the apex of an inferior ovary just beneath or outside the free portion of the corolla.

Comment: Found in flowers and fruits (cypsela) of the Asteraceae. May aid in dispersal by wind or animals. Considered by some to be an evolutionarily modified upper calyx portion, the lower portion having been incorporated into the floral tube casing adnate to the ovary wall; considered by others to be an outgrowth from the ovary wall.

FNA also has a term for "pappus scale": A pappus element that is more or less planate and relatively thin and broad; may terminate in one or more awn- or bristle-like appendages. I suggest we add a term for pappus element, with pappus scale, pappus awn, and pappus bristle as narrow synonyms.

proposed definition, pappus element: A cardinal organ part that is a segment of a pappus.

comment: May be awn-, scale-, or bristle-shaped.

synonyms: pappus scale, pappus awn, pappus bristle; part_of pappus

floral organ and floral whorl

GO refers to these terms, but they are absent from PO.

New terms and changes arising from previous discussions

seed (PO:0009010)

During a discussion at the POC meeting on 10-18-11, we realized that it would be best to have seed be a subtype of plant structure.

Current def.: A propagating organ formed in the reproductive cycle of gymnosperms and angiosperms, derived from the ovule and enclosing an embryo. [source: APWeb:Glossary, GR:Pankaj_Jaiswal] comment: The seed is representative of a next generation of sporophyte.

New proposed def.: A plant structure that develops from an ovule and contains an embryo enclosed in a seed coat.

Comment: A seed generally develops from an ovule after fertilization, but may develop without fertilization in the case of adventitious embryos, somatic embryos, or other embryos that arise through apogamy. A seed is a reproductive unit of seed plants (gymnosperms and angiosperms).

develops_from ovule, has_part embryo

Also removed seed part_of fruit relation, added seed to subsets for gymnosperms and angiosperms.

spore (PO:0025017)

Spore is_a cell, which is correct, but it is also a whole plant. Just as we changed the definition of plant zygote to reflect its dual nature, I suggest we change spore. Also suggest that we rename it plant spore, for consistency.

Current definition: A plant cell that arises through meiosis and develops into a gametophyte.

New proposed name and definition, plant spore: A single-celled whole plant that arises through meiosis and develops into a multi-celluar gametophyte.

Need to check if gametophytes are always multicellular in green algae.

plant spore stage (PO:0025375)

proposed definition: A gametophyte development stage that occurs during the interval between meiosis and the germination of a spore.

comment: The plant spore stage ends with the first cell division of a spore. Includes the stage when a megaspore is present before it develops into a megagametophyte or embryo sac and the stage when a microspore is present before it develops into a microgametophyte or pollen.

intersection of is_a gametophyte development stage, has_participant spore

plant spore dormant stage (PO:0025376)

proposed definition: A gametophyte dormant stage during which a spore participates in a dormancy process.

Comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.

is_a gametophyte dormant stage, has_participant spore

Because plant spore stage is an XP of is_a gametophyte development stage and has_participant spore, this will be inferred to be is_a plant spore stage.

plant embryo dormant stage (PO:0025377)

proposed definition: A sporophyte dormant stage during which a plant embryo participates in a dormancy process.

Comment: A dormancy process (GO:0022611) is a developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. In seed plants, a plant embryo dormant stage may be part of a seed dormant stage.

is_a sporophyte dormant stage, has_participant plant embryo

Since plant embryo stage is an XP of is_a sporophyte development stage and has_participant plant embryo, this will be inferred to be is_a plant embryo stage.

Also added seed dormant stage has_ part plant embryo dormant stage. Can't add the inverse part_of relation, because not all embryo dormancy occurs in seeds.

leaf lamina

Leaf lamina - now it is defined as any lamina that is part of a leaf, so petiole lamina is a subtype of leaf lamina. We should redefine this that the leaf lamina is a part exclusive of the petiole, because this is how most people think of it. Could add general term for "leaf part lamina" that would include leaf lamina and petiole lamina.

lobe and tooth

Last week we added the term "sinus" and agreed to add the related terms for tooth and margin.

Before we add those, we need to work on the organ margin terms a little.

proposed definition, lamina lobe: A cardinal organ part that is a rounded projection on the margin of an organ.

part_of lamina margin