POC Conf. Call 4-6-10

POC meeting,Webex Conference Call; Date: April 6th, 2010 10am (PDT)

Agenda:

Item carried over from last week's agenda:

1. Complete discussion of whorls:

Proposed new term: whorl (See SF Tracker: whorl)

Proposed def'n: A collective plant structure that consists of a ring of parts borne at the same node along an axis (LC test)

Child terms: perianth, phyllome whorl, androecium, gynoecium.

This would solve the issue of not putting androecium and gynoecium as children of phyllome whorl, and covering perianth.

From last week's discussion:

Phyllome whorl:(See SF Tracker: phyllome whorl)

Proposed new def'n: "A collective plant structure that contains phyllomes arranged around a common node." (minor rewording)

Child terms:calyx, corolla, epicalyx, leaf whorl

Note: phyllome whorl could include multiple whorls of phyllomes (for example; flowers that have mutliple whorls of petals (or other phyllomes).

2. New is_a children of cardinal organ part (See SF Tracker: New is_a children of cardinal organ part)

Several weeks ago, we created new children of cardinal organ part, from terms that had no is_a parent. We can deal with definitions and relationships of each term later, but for now we simply need to approve moving them to cardinal organ part.

Some of them can be dealt with later, but the terms listed here are a higher priority and/or can be dealt with very quickly. Many of the definitions need to be worked on at a future meeting. See Source Forge items for additional comments.

• At the Ithaca meeting on 12/2009, we decided to add a new term, stalk (See SF Tracker: stalk)

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 another cardinal organ part.

• pulvinus: (currently is_a (an) organ)

• receptacle: Part_of pedicel (which is currently a stalk, see below)

• stalk (moved from is_a organ)- A cardinal organ part that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part.

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

• leaf rachis (is_a stalk)-

-made a child of stalk (it had not is_a parent).

• peduncle: Is currently child of stalk, but perhaps it should be a child of stem?

• pedicel: Is currently child of stalk, but does not fit the definition. Should be a stem?

• hypanthium (made part_of receptacle instead of part_of flower)

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

Re-organization of existing terms

• floral bract and inflorescence bract

These two terms were children of both plant organ and bract (which is_a organ). Deleted is_a relationships to plant organ and kept under bract.

• fruit

Is a fruit an organ?

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

MAG: fruit fits our definition of a plant organ

• Embryo has no is_a parent

• Question from Laurel and Ramona about changing the references in OE when we rewrite the definitions of the terms (eg from MaizeGDB/TAIR to POC Curators)

X?. Upcoming Conferences and Meetings: Updates

• 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 may be going (?). Abstract/short paper submission deadline 4/15/10. Registration deadline May 28th, $325.

-Flash updates, up to 1 page: (short talks (5 min) giving the salient new developments on existing public ontologies) -Poster abstracts, up to 1 page (posters will be up for 2 days, with at least 1 poster session) Poster authors can also do a flash update.

Laurel and Ramona are preparing a short paper (up to 1 page) for submission to to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk.

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

Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene has been tentatively approved, waiting for details. Should hear in the next few days.

• Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island. Ramona presenting, Dennis attending, 15 minute oral presentation, Abstract submitted 3/26/10.

• 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.

from 3-23-10: 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 Alejandra and Ramona would check on the deadlines and Ramona will look into the req'ts for the symposium proposal.

• 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".

from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

• Annotation workshop/POC meeting to be held in Corvallis. Ramona will be in Portland June 26-29. Could have meeting one of those days (depending on when her talk is scheduled) or on June 30th. Who else can attend?

• Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.

11. Next meeting scheduled for Tuesday April 13th at 10am.