Agenda and Minutes 3-23-10

POC meeting, Date: March 23, 2010 Webex Conference Call

In attendance: Laurel Cooper, Ramona Walls (minutes), Pankaj Jaiswal, Alejandra Gandolfo, Dennis Stevenson. Absent: Chris Mungall, Barry Smith.

Minutes are added to agenda in italics under each item.

Items from last week's discussion:

1. Complete discussion of gametophyte, sporophyte and whole plant.

Does it make sense to have gametophyte and sporophyte be part_of whole plant? That way everything that is part of them, will automatically be part of whole plant. They are currently siblings, common is_a children of plant structures. Can one sibling term be a part_of another sibling???

Comments: BS: I do not see anything wrong with this.

We agreed to make gametophyte and sporophyte part_of whole plant. PJ suggested that we might need additional terms 'gametophyte whole plant' and 'sporophyte whole plant' as children of gametophyte and sporophyte. We decided to try out the existing structure for while, and later add those terms if we need them.

gametophyte

proposed def'n: A plant structure that arises through meiosis and may produce gametes by mitosis (POC conf call, 3-16-10)

sporophyte

proposed def'n: A plant structure that is a product of fertilization and produces spores through meiosis.(POC conf call, 3-16-10)

Comment: the gametophyte arises from the product of meiosis (the spore)

whole plant

proposed def'n: A plant structure which is a whole organism (from POC meeting in Ithaca, Dec 09)

On the conference calls on Feb 16th and 23rd, we had fairly extensive discussions of the functionality of keeping gametophyte and sporophyte as siblings to whole plant.

We agreed that our guiding principles should be:

• have general terms for all structures that would be part_of whole plant

A few examples of whole plant are embryo and seed.

We all agreed that the proposed definitions of gametophyte, sporophyte, and whole plant we acceptable, and decided to close the items on Source Forge.

2. Complete discussion of cardinal organ part and collective organ

Are the definitions finalized?

Ramona and Laurel moved a group of terms so they are now children of these two structures. These include all the terms that don't have is_a parents and are appropriate, plus a few others (see below:)

Note: The existing part_of relationships were retained except as noted below. These have been posted on SF for comments.

a. new children of cardinal organ part

• raphe (removed part_of link to ovary, because it is part of the funicle that is attached to the ovary, not part of the ovary)

• antiraphe

proposed def'n: The side (or part) of the ovule (or seed) that is opposite the raphe. (made is_a child of cardinal organ part, because it is part_of ovule).

• organ margin

• leaf lamina margin

Currently: PO:0020128 leaf margin (synonym leaf lamina margin): The margin or edge of the lamina. [source: UMSL:fz]

I suggest making this term is_a child of organ margin.

I also using the term leaf lamina margin, because it fits with the definition better.

• leaf lamina base

• stalk (moved from is_a organ)

• leaf rachis (is_a stalk)

• peduncle

• pulvinus (currently is_a organ)

• fruit (is a fruit an organ?) MAG: fruit fits our definition of a plant organ

• floral bract and inflorescence bract (were children of both plant organ and bract (which is_a organ).

Deleted is_a relationships to plant organ and kept under bract).

• hypanthium (made part_of receptacle instead of part_of flower)

comment: LC: I think it is better to leave hypanthium as part_of flower.

• receptacle (part of pedicel, but pedicel is currently not an organ)

• pedicel (is currently child of stalk, but does not fit the definition. Should be a stem?)

b. new children of collective plant structure:

No definitions or part_of relationships have been changed.

New terms. Posted on SourceForge tracker for comments.

3. spore:

proposed def'n: A reproductive cell, usually unicellular, capable of developing into an adult without fusion with another cell. (Raven, Evert, Eichorn, 4th Ed)

comments: the product of meiosis, is_a plant cell, parent of megaspore, microspore, develops into the gametophyte

At the Ithaca meeting, we proposed having simple plant organ and compound plant organ as children of plant organ.

4. simple organ

Proposed def'n: A plant organ that does not contain any other plant organ as a part.

Examples: petal, root, simple leaf. [source: rw:test]

Comment: This term may not be necessary with our current definition of plant organ (RW)

5. compound organ

Proposed def'n: plant organ that has as its parts two or more simple plant organs.

Example: fern sorus composed of multiple sporangia or gyneocium composed of multiple carpels.

Comment: This term may not be necessary with our current definitions of plant organ and collective plant structure (RW).

6. Upcoming Conferences and Meetings:

• American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, mini symposium presentation (hopefully) or poster and annotation workshop with Gramene. Abstract submitted 3/12/10

• Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island. Ramona, Dennis going (?), 12 minute oral presentation, Abstract submission deadline 4/1/10.

• Bio-Ontologies 2010: Semantic Applications in Life Sciences. July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona going (?). Abstract/short paper submission deadline 4/15/10.

• International Society for Computational Biology (ISCB). July 10th-13th, 2010. Boston, Mass. Laurel going (?).

• International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm): "Call of symposia closes" 3-31-10, Abstracts submission deadline: 12-1-10.

• Latin American Congress of Botany (http://www.botanica-alb.org/X_Congreso/index.php). La Serena, Chile, October 4-10; MAG: "I am not sure about due dates for this one due to the earthquake".

• Annotation workshops to be held at NYBG and Corvallis. Dates need to be discussed. Ramona will be visiting in Corvallis around the end of June.

7. Next conference call- Would it work to change next week to Thursday and do it at 10am?

Thursday April 1st- 10am? PDT.