POC Conf. Call 1-17-12

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

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No regular meeting will take place this week, but those who are around will meet to review some terms definitions.

Term Requests from Agron-Omics

At the recent EBI Crop Ontology meeting PJ met with Sean Walsh Arabidopsis GROwth Network integrating OMICS technologies

Vascular tissue:

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

proposed new def'n: 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

Other

We also have a request for pappus from Shawna Thompson. Don't know if it is related to these.

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.