POC Conf. Call 4-6-10

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

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls(NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico,

Rex Nelson-Soybase, USDA-ARS, Ames, Iowa

Absent: Alejandra Gandolfo, Cornell University, Pankaj Jaiswal (OSU)

Agenda:

Minutes are in italics below each agenda item.

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

Minutes were accepted by all present at the beginning of the call.

Item carried over from last week's agenda:

1. Complete discussion of whorls:

Proposed new term: whorl structure: proposed definition: A collective plant structure composed of one or more whorls. (See SF Tracker: whorl structure).

Children will be whorl, perianth, corolla, androecium, etc.

On the conf call, we decided that it was redundant to have the child term 'phyllome whorl' structure because all whorl structures were composed of phyllomes, so this term should be obsoleted. We can add it later if we find otherwise. This would solve the issue of not putting androecium and gynoecium as children of phyllome whorl, and covering perianth.

In discussions after the webex call, PJ suggested this should be called: 'whorled plant structure' and instead of the new term 'whorl', we should keep 'phyllome whorl'.

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).

We discussed structures that can contain multiple whorls, like corolla or perianth, and agreed that by definition, a whorl cannot contain multiple whorls. We decided to add a structure that would encompass these and be a child of collective plant structure:

We also worked on the definition of whorl:

Whorl: proposed def'n: A collective plant structure that consists of two or more plant organs of the same type borne at the same node (POC Curators). (See SF Tracker: whorl)

We also discussed how to deal with whorls that have been reduced to a single organ. Decided to keep definitions of CPS and whorl as is, and place reduced structures under plant organ. We will need to remember to add link to the homologous terms under whorl. For example, if a flower only contains one carpel, we could add a term like "simple gynoecium" as a child of plant organ with a cross reference to gynoecium. DWS said this should only be an issue for reproductive parts, since there are no flowers with a single petal. What about sepals?

Items 2 and 3 were postponed to future meetings.

2. stalk (See SF Tracker: stalk)

This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.

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 an 
organ or another cardinal organ part.

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

Proposed children of stalk: (Test: do all of these fit the definition?)

• filament: The stalk of a stamen.(stamen:organ)

• petiole: The stalk of a leaf. (leaf:organ)

• petiolule: The stalk of a leaflet (leaflet:cardinal organ part)

• funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)

• gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)

• leaf rachis: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ) (See SF Tracker: leaf rachis)

• peduncle: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves. (See SF Tracker: peduncle)

propose revised def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).

• pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

(See SF Tracker: pedicel)

propose revised def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).

Note: We also have the term 'stem'. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.

Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary] Synonyms: cane, culm, stalk, trunk

Problem: Stem has no is_a parent- should be a collective plant structure? OR If we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks

Based on this definition, I think pedicel and peduncle are better as stalks.

3. More '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.

*receptacle: The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators]. (See SF Tracker: receptacle)

propose revised def'n: The region at the top of either the peduncle or pedicel where the floral appendages (for example, sepals, petals, stamens, and pistils) are attached.(Brooklyn Botanic Garden http://www.bbg.org/gar2/topics/botany/parts_flowers.html)

Comments: If both pedicel and peduncle is_a stalk, and stalk is_a 'cardinal organ part', then both pedicel and peduncle must be part of some organ for this to work.

*hypanthium- A cup- or tube-like structure bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary of a flower. (See SF Tracker: hypanthium)

made part_of receptacle instead of part_of flower

*pulvinus:-A more or less abrupt swelling, especially at the apex or base of a petiole or leaf sheath, often glandular and/or being the place where a plant responds to touch, gravity or light, in panicoid grasses a swollen region in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary] (See SF Tracker: pulvinus)

-currently is_a (an) organ

4. Re-organization of existing terms

*floral bract and inflorescence bract (See SF Tracker: 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. Everyone agreed this made sense. CM suggested using OBO-Edit to search for redundant links using the Reasoner.

* fruit (See SF Tracker: fruit)

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

Is a fruit an organ? MAG: fruit fits our definition of a plant organ (from 3-23-10).

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).

We had extensive discussion about the nature of fruit- whether or not it always was composed of two or more carpels? Examples discussed were oranges- each segment is a carpel, pineapples- the whole inflorescence, strawberries and raspberries- multiple carpels more or less fused together, from a single flower

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

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

5. 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). What is the correct protocol for doing this?

6. 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. . 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. Abstract/short paper submission deadline 4/15/10

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, poster 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): "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. DWS: Deadline for symposia has been extended to April 9th and possibly till the end of the month. Each attendee can only present one paper. DWS is already committed to presenting the on the 'Tree of Life Project'. Ramona and Laurel could present. 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?

Dennis is interested in also coming out, what about Barry, Chris and Alejandra? Pankaj would like to also include Aaron Liston and Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).

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

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