POC Conf. Call 5-4-10

POC meeting, Webex Conference Call; Date: May 4th, 2010 10am (PDT)

Minutes are in italics below each agenda item.

In attendance: POC members: Laurel Cooper (OSU), Alejandra Gandolfo, (Cornell University), Ramona Walls (NYBG)

Collaborators: Rex Nelson-SOYbase, USDA-ARS, Ames, Iowa, Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico,

Absent: Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Agenda:

Acceptance of the minutes from last weeks meeting? All in favor? There were no additions, deletions or changes to last weeks minutes.

Items carried over from last week's agenda:

1. Wrapping up the phyllome structures that include 'whorls' and 'rosettes':

collective phyllome structure (See SF tracker: collective phyllome structure).

New proposed def'n.:A collective plant structure that consists of two or more phyllomes originating from the same node or from two or more adjacent nodes with compressed internodes.

This def'n avoids the use of the term 'stem' here. 'Whorl' and 'floral whorl' (a term used in GO) are narrow synonyms.

This definition was approved by all present. The item will be accepted and closed on Source Forge.

2. fruit (See SF Tracker: fruit)

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

Proposed def'n: A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it.

PJ (via SourceForge) offered a proposed def'n using 'post-fertilization'.

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).

POC conf call: 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: exception parthenocarpy or other hormone-induced condition)

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it).

3. Embryo (See SF Tracker: embryo)

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A young sporophyte before the period of rapid growth. [source: Raven et al.]

Comments: (1) In seed plants, germination marks the end of the embryonic phase.

(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes

Relationships:

(1) has no is_a parent, propose making it is_a whole plant?

(2) develops_from zygote (see comment above)

(3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)

Parentage: Those present agreed that it might be better to have embryo is_a sporphyte, which makes it a whole plant through transitivity. Usually develops_from zygote

Also agreed that the phrase 'before the period of rapid growth' is too vague.

POC Conf call: A young sporophyte before the period of rapid growth.

This term will remain open as the def'n needs further refinement.

4. 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)

For group discussion:

-Plant cell child terms: organization, completeness, definitions. Are we happy with them, or do we plan on a major overhaul?

-- PO browser with all cell types expanded

- List of PO plant cell types that are not in the Cell.obo file (thanks Rex!). Do we want to request that these terms be included in the CL?

- Need to think about tissues and organs that we and CL might want to use for cross-product definitions.

- Should we aim for complete redundancy between cells in PO and plant cells in CL?

Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting. Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.

The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.

In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.

Laurel and/or Ramona will give a 10-15 minute presentation at the Cell Ontology meeting.

* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.

Pankaj suggested we plan on meeting for two days. Dennis can make June 30th, but has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th.

Alejandra cannot travel that day -- can attend via conference call.

Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th. Ramona has sent a request to schedule her talk on the 27th or 28th. Barry will be in France this week and can't attend. What about 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 are registered.

-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.

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation and Annotation Workshop with Gramene.

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 is scheduled for Saturday July 31, 8am-12pm. more details TBA

* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):

Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.

Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with internet for outreach activities.

Pankaj will be co-organizer with Ramona. Laurel and Ramona are interested in going and speaking if funds are available.

Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.

• 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 May 11th at 10am PDT.