Minutes POC Conf Call 4-1-10

POC meeting,Webex Conference Call; Date: April 1, 2010 10am

In attendance: Laurel Cooper (minutes), Ramona Walls, Pankaj Jaiswal, Alejandra Gandolfo, Dennis Stevenson. Absent: Chris Mungall, Barry Smith.

Minutes are added to agenda in italics under each item.

New terms. Posted on SourceForge tracker for comments.

At the Ithaca meeting, we proposed having simple plant organ and compound plant organ as children of plant organ. We need to decide if it is necessary to retain these terms, now that we have collective plant structure.

1. simple organ (See SF Tracker: simple plant 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, since it is covered by our current definition of plant organ (RW)

2. compound organ (See SF Tracker: compound plant organ)

Proposed def'n: Compound organ: 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, also compound leaf.

Comment: This term may not be necessary, since it is covered by our current definition collective plant structure (RW).

After quite a bit of discussion, we decided that the terms:'simple and compound' are actually phenotypic qualifiers from PATO, so we do not need to keep these as separate terms. Since these terms were only added after the Ithaca meeting, they have no annotations associated with them yet and they will be obsoleted.

3. spore: (See SF Tracker: spore)

This term is currently missing from the PO. We need to come up with a definition.

Raven,Evert, Eichorn, 4th Ed defines it as: A reproductive cell, usually unicellular, capable of developing into an adult without fusion with another cell.

proposed def'n: A plant cell that arises through meiosis and develops into the gametophyte.

comments: the product of meiosis, is_a plant cell, parent of megaspore, microspore, develops into the gametophyte

We discussed the cases in fungi and algae where a 'spore' might be the product of the fusion of two gametes (zygospores). In this case, zygospore can be a synonym of zygote. We agreed to define it as: final def'n: A plant cell that arises through meiosis and develops into a gametophyte. This will be added as a new term, as above.

Item from last week's agenda:

4. New is_a children of collective plant structure: (See SF Tracker: New is_a children of collective plant structure)

(collective plant structure def'n: A plant structure that is a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue.)

We can deal with definitions and relationships of each term later, but for now we simply need to approve moving them to 'children of collective plant structure'. These terms had no is_a parents.

No definitions or part_of relationships have been changed.

• andreocium- "Collectively, the stamens of one flower."

• calyx- "The sepals of one flower collectively."

• corolla- "The petals of a flower collectively."

• epicalyx-"A whorl of structures immediately outside the calyx whorl."

• flower- "A heterosporangiate strobilus, typically consisting of androecium, gynoecium, usually surrounded by a perianth and borne on an axis or receptacle."

• gynoecium- "Collectively the carpels of a flower."

• inflorescence-"That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers."

• infructescence- "The grouping or arrangement in which fruits are borne on a plant."

• involucre- "A whorl of bracts at the base of a cluster of flowers as found in Asteraceae or Compositae. (we discussed that this is not actually a whorl, but a spiral arrangement of bracts)"

• perianth- "Non-fertile parts of a flower surrounding the fertile organs, collectively the calyx and corolla of a flower, or only a single whorl."

• spikelet- "Ultimate and congested inflorescence branch of the grasses."

Everyone agreed that these terms should be children of collective plant structure and that we will come back and work on the definitions at a future date

• phyllome whorl (See SF Tracker: phyllome whorl)

This term is a special case since it was previously a child of phyllome (was is_a phyllome)(probably incorrectly). Old def'n: "A circular arrangement of phyllome".

We had an extensive discussion regarding the definition and the relationships and decided that we should retain this term as a child of CPS and make corolla, calyx and epicalyx its children. Perhaps androecium and gynoecium should also be children of phyllome whorl? We need to come back and work on the child terms of phyllome whorl.

New def'n: A CPS that is an arrangement of phyllomes attached at a common node.

5. Organ margin (See SF Tracker: organ margin)

This term was discussed on last week's conference call.

Proposed def'n: The edge of an organ and the area immediately internally adjacent to it.

-Added new is_a children for all appropriate children of phyllome, that is, all laminar structures. These are new terms (except for sepal, leaflet and leaf margin)-

The group all agreed that we do not we to create SF tracker items for these.

from Dev browser:

• PO:0025008: petal margin
• PO:0025011: bract margin
• PO:0025012: cotyledon margin
• PO:0025013: prophyll margin
• PO:0025014: scale leaf margin
• PO:0025016: sporophyll margin
• PO:0025015: tepal margin
• PO:0005021: sepal margin
• PO:0020128: leaf margin
• PO:0006034: leaflet margin (leaflet is_a cardinal organ part), should be is_a leaf margin

Comments: Need to add a term for phyllome margin, and make appropriate relationships to the children of phyllome. Also need to create stamen margin and carpel margin and add comment that only flattened stamens or carpels can have a margin (as with petiole margin).

6. Leaf margin: (See SF Tracker: leaf margin)

Proposed def'n: The margin of any flattened portion of a leaf.

- will have children 'leaf lamina margin' and 'leaf petiole margin' .

• PO:0025009: leaf lamina margin
• PO:0025010: petiole margin

We agreed that this term should be is_a organ margin. Will also make leaflet margin a child of leaf margin.

7. Re-organization of existing terms Tabled for next week's discussion.

• 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

8. Outreach page on PO wiki

The outreach page on the PO wiki has been updated with abstracts. See: http://wiki.plantontology.org:8080/index.php/POC_Outreach_Events. We will continue to keep this updated so people can have quick access to abstracts and outreach activities.

Question: There is a similar page on the POC website- http://www.plantontology.org/docs/otherdocs/poc_outreach.html

Maybe we could have both links go to the same place, so we don't have to keep two pages updated? Pankaj siad it was fine to have a link to the PO Wiki Outreach page on the POC webpage. Laurel will look after.

Also: POC Homepage (http://www.plantontology.org) has been updated with upcoming presentations.

9. 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.

We need to discuss what would be the most appropriate type of presentation for this meeting; there are 3 categories:

-Short papers, up to 4 pages: (for ~20 minute presentation, if selected, and publication in the Proceedings booklet)

-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.

Everyone agreed that is would make the most sense for Laurel and Ramona to prepare 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.

• International Society for Computational Biology (ISCB). July 10th-13th, 2010. Boston, Mass. This is directly after the Bio-Ontologies meeting, but both Laurel and Ramona felt its not really worth the time and money (Reg'n = ~$900) to stay for this part.

• 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 6th at 10am Back to our normal day, Tuesday and we will meet at 10am (PDT), unless it is a problem for PJ.