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. Rosemary Shrestha joined in but without audio. 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, CM (by email): I do not see anything wrong with this.

We agreed to make gametophyte and sporophyte part_of whole plant. Pankaj 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 were acceptable, and decided to close the items on Source Forge.

2. Complete discussion of cardinal organ part and collective plant structure

Are the definitions finalized?

The group agreed that the definitions were acceptable, and we should close the items on Source Forge. We will put a comment under collective plant structure that the organs can be of the same or different types. Also, we will give the PO ids of the examples and add hyperlinks to those terms (should try to do this whenever examples are used in the comments).

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?)

Dennis suggested that we should prioritize our discussion of terms so that we can deal first with the terms that people are most likely to need/use, then address little-used terms (like antiraphe) as time allows. We agreed this was a good idea.

This week, we dealt with organ margin and leaf lamina margin.

Proposed definition: Organ margin: The edge of an organ and the area immediately internally adjacent to it.

We discussed which organs can have margins, and agreed that it was only flattened or laminar organs or organ parts, since only they have an edge.

Proposed definition: Leaf margin: The margin of any flattened portion of a leaf.

Rather than changing leaf margin to leaf lamina margin (as proposed by RW on SourceForge), the current term 'leaf margin' should remain, and the synonym 'leaf lamina margin' should be removed. Instead, leaf margin should have is_a children 'leaf lamina margin' and 'petiole margin' (for flattened or marginal petioles).

Proposed definition: Leaf lamina margin: The margin of a leaf lamina

Proposed definition: Petiole margin: The margin of a flattened petiole. Comment: only marginal or laminar petioles can have a margin.

We will need to add margins for all other laminar structures, probably most of the children of 'phyllome.' We already have sepal margin and petal margin.

On a related note, petal and sepal should be children of phyllome.

Discussion of other cardinal organ parts was postponed until future meetings.

Items 2b through 5 were postponed for future meetings.

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.

Laurel is looking into the possibility of hosting a booth with other database groups, for example SGN, TAIR. Gramene. She is looking into costs and interest. We should prepare a brochure to distribute, similar to the one Gramene has.

• 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.

BSA abstract will be submitted this week, Ramona will send out draft for comments first.

• 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.

Lol and Ramona will prepare a short paper for submission to to Bio-Ontologies meeting.

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

Laurel considering going, if there is useful information.

• 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.

Dennis and Alejandra are planning to attend IBC2011. Dennis will work on possible symposium proposals. Pankaj can be co-organizer if necessary. Need 4-6 speakers for the symposium. Laurel and Ramona are interested in going if funds are available

• Latin American Congress of Botany (LACB) (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".

Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

• 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.

We discussed possibly having an annotation workshop and/or POC meeting in Corvallis in late June/July. Ramona will be in Portland June 26-29 for the Evolution meetings, so we could have the meeting one of those days, or on the 30th (depending on the date that Ramona's talk is scheduled). Dennis may be able to come at that time. Have to check with others. We also discussed having a half-day annotation workshop at the NYBG in the fall. At that time, we could also invite experts from different taxa to comment/advise on the latest version of the PO.

Pankaj suggested posting abstracts on the PO wiki. Ramona and Lol will add these to the Outreach page.

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

Thursday April 1st- 10am? PDT.

Doodle poll will be sent around.