POC Conf. Call 4-20-10

POC meeting, Webex Conference Call; Date: April 20th, 2010 10am (PDT)

Agenda:

Acceptance of the minutes from last weeks meeting? All in favor?

1. Wrapping up the 'whorls' and 'rosettes':

A. phyllome aggregation: (See SF tracker: phyllome aggregation).

Proposed def.:A collective plant structure that contains two or more phyllomes arranged along the plant axis in either one or more whorled arrangements or in a rosette.

This would replace the term whorled phyllome structure:(See SF Tracker: whorled phyllome structure) with the proposed new def'n:: A collective plant structure that contains one or more whorled arrangements of phyllomes.

Children are androecium, calyx, corolla, epicalyx, gynoecium, leaf whorl, perianth, rosette, and tepal aggregation (see item B).

Note: Whorls that have been reduced to a single organ will be placed under 'plant organ'.

B. Children of phyllome aggregation: See SF tracker item (new defintions for children of whorled phyllome structure)and items C and D below.

>>Androecium: A phyllome aggregation composed of two or more stamens. >>Calyx: A phyllome aggregation composed of two or more sepals. >>Corolla: A phyllome aggregation structure composed of two or more petals. >>Epicalyx: A phyllome aggregation composed of two or more phyllomes immediately outside the calyx. >>Gynoecium: A phyllome aggregation composed of two or more carpels. >>Leaf whorl: A phyllome aggregation composed of two or more leaves arising from the same node. >>Perianth: A phyllome aggregation composed of two or more petals, sepals, or tepals. >>Tepal aggregation: A phyllome aggregation composed of four or more tepals either in a rosette or in two or more whorled arrangements.

C. New term: Rosette: (see SF tracker item rosette)

Proposed def.: A collective plant structure that contains multiple plant structures of the same type borne in a helix along an axis with compressed internodes.

D. New term: whorled tepal structure: (See SF Tracker whorled tepal structure)

proposed new def'n: 'whorled tepal structure': A whorled phyllome structure that is composed of two or more tepals

This could be replaced by tepal aggregation: A phyllome aggregation composed of four or more tepals either in a rosette or in two or more whorled arrangements.

Can we close the SF trackers for these terms and move on (Please!)?

E. tepal (See SF Tracker: tepal)

proposed revised def'n: A phyllome that is part of a perianth in which all parts are similar in appearance and are neither petals nor sepals.

Check out the link to images for tepals on the dev browser: tepal

Item carried over from last week's agenda:

2. fruit (See SF Tracker: fruit)

Is a fruit an organ?

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

proposed definition (modified slightly from Gleason and Cronquist 2nd edition, via Dennis): A collective plant structure that contains a ripened ovary, together with any other structures that ripen with it and form a unit with it.

proposed change: fruit is_a 'collective plant structure' and part_of infructescence. (CPS: a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue).

3. Embryo (See SF Tracker: embryo) Def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

-has no is_a parent, propose making it is_a whole plant?

5. Upcoming Conferences and Meetings: Updates

• Cell Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME. Laurel and Ramona will attend.

Scientific agenda will include:

1) Review and discussion of the ongoing work on specific areas of the Cell Ontology

2) Resolution of issues regarding the high level structure of the Cell Ontology

3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms

4) Organization of outreach efforts to import cell type terms from other ontologies and resources

5) Discussion about software enhancements to the AmiGO tool to enable and search of GO annotations that involve coannotation to CL terms

6) Applications of the CL (Cell Ontology)

Agreed that there should be some group discussion of plant cells before this meeting.Laurel and Ramona will review the Cell Ontology.

• POC meeting/Annotation workshop to be held in Corvallis on June 30th. Ramona will be in Portland June 26-29.

Dennis can make June 30th, but Alejandra cannot travel that day -- can attend via conference call What about Barry and Chris?

Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).

• 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.

-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 submitted the 1 pager on Friday April 16th to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. We will be notified by May 7th if we are doing a flash update. Registration deadline May 28th, $325.

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, mini symposium presentation. 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 for Sunday Aug 1, 8am-12pm. more details TBA

• 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):

Dennis and Alejandra are planning to attend IBC2011. Pankaj can be co-organizer if necessary. 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.

Updates?

• Each symposium consists of six 20 minute sessions. Each person can give only one talk at the meeting, and can be an organizer for only one meeting. Each meeting must have two organizers. Speakers must cover their own travel costs. Organizers should emphasize broad international participation and appropriate gender balance.

Symposium proposal consists of:

• details of each proposed symposium including contact details of participants.
• a maximum of 500 words to describe the scientific content.

Dennis is presenting in another symposium, but is not an organizer, so can organize an ontology symposium but not present. Some discussion of who presenters should be -- maybe Pankaj, Laurel and Ramona, Barry or Chris, someone from another plant-based ontology - perhaps Rex or Rosemary?

Ramona has sent out a draft proposal for review before the week's meeting Comments?

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

8. Next meeting scheduled for Tuesday April 27th at 10am.