POC Conf. Call 5-25-10

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POC meeting, Webex Conference Call; Date: May 25th, 2010 10am (PDT)


Acceptance of the minutes from the 5-11-10 meeting? All in favor?


Agenda:

1. Report from the Cell Type Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME.

Laurel and Ramona will attend and will give a 10-15 minute presentation.

Browse Cell Type Ontology on BioPortal



2. Meeting with Plant Trait Ontology people.

Ramona has scheduled a tentative meeting with Dan Bunker (College of NJ) and Farshid Ahrestani (Columbia) to discuss possible collaborations with PO. Want to find out why they are developing their own ontology rather than using PO and working within OBO


Items carried over from previous week's agenda:

Items carried over from last week's agenda:


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)

Discussion of embryo was postponed until next meeting.


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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