POC Conf. Call 4-27-10

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POC meeting, Webex Conference Call; Date: April 27th, 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), Dennis Stevenson (NYBG)

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


Agenda:

Acceptance of the minutes from last weeks meeting? All in favor? Minutes from 4-20-10 were accepted without changes.


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


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

Proposed def.:A collective plant structure that consists of two or more phyllomes originating on the stem from the same node or from two or more adjacent nodes with compressed internodes.

Unlike the definition we came up with last week, this definitions does not contain the undefined terms rosette and whorl. It also uses the term 'stem' instead of 'axis', because 'stem' is defined in the PO, and axis is not.

There was discussion about whether it was appropriate to use the term 'stem' here although all agreed that it was better than axis. Alejandra made the comment that when referring to the reproductive structures of the conifers; the cones, "axis" is used to define the central portion of the cones where the sporophylls (micro and mega) are spirally arranged. This is also valid for other "structures" such as the strobili of the lycopods. Those are not considered to be "stems" they are axes

We will make a note to work on the definition of 'stem'- it is on the agenda for May 4th Conf Call.


'Collective phyllome structure' would replace the original term 'phyllome whorl' (PO:0008033) which we have been calling 'whorled phyllome structure.'

Note: The original term 'phyllome whorl'(PO:0008033) will be merged into the new term 'collective phyllome structure', which will have a new ID#. The old name and ID # will be listed as an alternate (secondary) ID.

The proposed new term phyllome aggregation would be rejected. All agreed that this term should be rejected and closed.


'Whorl' and 'floral whorl' (a term used in GO) would be narrow synonyms. All agreed


Children (see items 2 and 3 below) are androecium, calyx, corolla, epicalyx, gynoecium, collective leaf structure, perianth and collective tepal structure (new term proposed by Laurel and Pankaj after the meeting).


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

See comments below under androecium and gynoecium.


2. Children of collective phyllome structure: See SF tracker item new definitions for children of collective phyllome structure and item C below.


>>androecium: A collective phyllome structure composed of two or more stamens.

>>gynoecium: A collective phyllome structure composed of two or more carpels.

There was discussion about whether or not the androecium and gynoecium were in fact collective structures, or could include the case where there was only one anther or carpel. We decided that it was not the typical case and it could be added in a comment.

>>calyx: A collective phyllome structure composed of two or more sepals.

>>corolla: A collective phyllome structure composed of two or more petals.

>>epicalyx: A collective phyllome structure composed of two or more phyllomes immediately outside the calyx.

>>collective leaf structure: A collective phyllome structure composed of two or more leaves. Rosette and leaf whorl are synonyms.

>>perianth: A collective phyllome structure composed of two or more petals, sepals, or tepals.

>>collective tepal structure: A perianth composed of two or more tepals (Child of perianth, see item C below).

All agreed


The proposed children rosette and whorl would be rejected. Rosette and leaf whorl would be synonyms of 'collective leaf structure' and whorl would be a synonym of 'collective phyllome structure'.

All agreed these terms should be rejected and closed on SF.


  • The previously-used term: Leaf whorl (PO:0008034) was made obsolete, because its definition did not match the new ontology structure as a child of collective phyllome structure. Annotations for this term are now associated with the new term collective leaf structure (PO:0025022).

All agreed that it was appropriate to obsolete 'leaf whorl'.


3. New term: collective tepal structure: (See SF Tracker collective tepal structure)

proposed new def'n: A perianth composed of two or more tepals.

is_a perianth

All agreed


4. 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.

All agreed


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

What do folks think of this as a way to include images in the PO? Is there a way to include images in the obo file?

Ramona showed us how she is linking to the images at PlantSystematics.org. This is the site where the majority of the images will be kept that are generated at NYBG and Cornell. We are working on figuring out the best way to link to these images in the AmiGO browser.

Update from Alejandra: She has replaced her undergraduates with a technician who is coming twice a week to help with cataloging the images in the slide collections. They will be labeled with bar codes to facilitate searching. Anticipates making better progress now.


Items carried over from last week's agenda:

5. fruit (See SF Tracker: fruit)

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.


Does everyone agree that a fruit is a collective plant structure? All agreed

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).

PJ (via SourceForge) commented that 'ripe' should not be used here and offered a proposed def'n using 'post-fertilization'. We came up with a 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. We will continue these discussions next week.


Item 6 was tabled for next weeks discussion.

6. 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?

-embryo contained_in archegonium could work for all land plants (not charophytes), rather than contained_in seed (doi: 10.1111/j.1469-8137.2009.03054.x)


7. 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.

Rex sent in a list of PO plant cell that are not in the Cell.obo file (thanks Rex!). Ramona and I will look at these and we should talk about the cell ontology at next weeks 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 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, 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 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?

Alejandra said she talked to the organizers, and we only need to submit 2 or 3 potential speakers. The others can be selected from the abstracts submitted to the meeting. Laurel and Ramona are happy to be organizers and are interested in attending if the funding is available. Pankaj will check with NSF to see if we can use travel funds for an international meeting.

Ramona has circulated a proposal to be submitted by Friday April 30th. There were a few comments about the idea to include a hands on workshop- Ramona will follow up with the organizers about whether or not this is a possibility. Laurel will confirm whether she or Pankaj will be co-organizer with Ramona. Ramona will contact someone from the Genomics of Seed Plants project about being a potential speaker.


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 4th at 10am.

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