POC Conf. Call 6-30-10

POC meeting, Webex Conference Call; Date: June 30th, 2010 10am (PDT)

In attendance: POC members:

Collaborators:

Absent:

Acceptance of the minutes from the 6-29-10 meeting? All in favor?

Workshop page: [Corvallis Workshop June 29th and 30th, 2010]

*Work on items from Tuesday morning:

-Ontology development

Updates of upper level terms

bud

Tuber

cortex- hypodermis and endodermis

1. stem (PO:0009047)

stem

Problem: Stem has no is_a parent- should be a collective plant structure or a plant organ?

Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]

Synonyms: cane, culm, stalk, trunk

OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.

The axis that is above ground, as well as anatomically similar portions below ground, such as rhizomes or corms.

2. Shoot (PO:0009006)

shoot

current def'n: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems. [source: POC:curators]

Problem: Shoot has no is_a parent- should be a collective plant structure or a plant organ?

3. Tuber terms(PO:0004543)

tuber

see comments from 6-29 meeting

We should request the term determinate from PATO. Tuber is already defined as determinate growth.

• Subterranean tuber (PO:0004547)

is_a 'tuber' and part_of 'rhizome'

current def'n: A swollen rhizome or a part of the rhizome with determinate growth. [source: POC:curator]

proposed def'n: A tuber that is part of a rhizome.

• aerial tuber (PO:0004548)

current def'n: An axillary shoot with a swollen stem.

4. rhizome (PO:0004542)

(need to add link to SF tracker)

Current def'n: Underground shoot. [source: POC:curators]'

5. Stolon (PO:0003024)

(need to add link to SF tracker)

current def'n: A slender, prostrate or trailing above-ground stem which produces roots and sometimes erect shoots at its nodes. [source: APWeb:Glossary]

but it is classified as a shoot.

6. stalk (PO:0025066)

(See SF Tracker: stalk)

This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.

current def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.

Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.

-made it a child of cardinal organ part (as per its definition) rather than an organ.

Proposed children of stalk: (Test: do all of these fit the definition?)

• filament: The stalk of a stamen.(stamen:organ)

• petiole: The stalk of a leaf. (leaf:organ)

• petiolule: The stalk of a leaflet (leaflet:cardinal organ part)

• funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)

• gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)

• leaf rachis: (See SF Tracker: leaf rachis)

current def'n: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ)

• peduncle: (peduncle)

current def'n: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves.

proposed def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).

• pedicel: (See SF Tracker: pedicel)

current def'n: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

proposed def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).

Note: We also have the term 'stem'. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.

Terms from last week

1. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.

Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312

Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.

2. Embryo (See SF Tracker: embryo)

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants

(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes -add a comment?

Relationships:

(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity (2) develops_from zygote (see comment above) Usually (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)

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