POC Conf. Call 12-11-12
POC meeting, Webex Conference Call; Date: Tuesday Dec 11th, 2012 10am PST/1pm EST
In attendance:
Plans for Upcoming Release #19
Timeline for Release: Goal is mid December 2012 Release_19
Priorities for inclusion in the Release:
- Revisions to PSDS:
- Fruit development stages
- New datasets: grape, cotton, rice
LC: will send MAG and YY a list of the new PAE terms that we need translations for.
Goal: is to complete the edits and annotation sets by Friday Dec 7th, then load the database over the weekend onto beta. That will give us the following week to troubleshoot issues and hopefully have it completed by Dec 14th.
Open trackers: To be fixed:
We need to fix this definition, as it currently only includes angiosperms:
Current name and def'n:
generative cell (PO:0020097): A cell of the male gametophyte of angiosperms that divides to produce two male gametes or sperm cells. [source: APweb:Glossary]
Definitions from Raven 5th ed: generative cell: 1. In gymnosperms, the cell of the male gametophyte that divides to form the sterile and spermatogenous cells
2. In angiosperms, the cell of the male gametophyte that divides to form two sperm
spermatogenous cell: the cell of the male gametophyte or pollen grain of gymnosperms, which divides to form 2 sperm cells
Originally we proposed changing generative cell (PO:0020097) to a spermatogenous cell and make generative cell a synonym of it, but a different solution is below:
Propose new parent term spermatogenous cell, which would encompass the spermatogenous cells in the lower plants and would have child terms: 'generative cell' (PO:0020097) for angiosperms, and 'body cell' (new PO:0025526) for the gymnosperms.
spermatogenous cell (new; PO:0025525): A plant cell (PO:0009002) that gives rise to one or more plant sperm cells (PO:0000084).
generative cell (PO:0020097): A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280)in angiosperms, that divides to produce two pollen sperm cells (PO:0025121) in angiosperms.
body cell (new; PO:0025525): A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280) in gymnosperms, that divides to produce the sterile and pollen sperm cells (PO:0025121).
add broad synonym: generative cell
Question: Can we define the pollen sperm cell (PO:0025121) as: A plant sperm cell (PO:0000084) that develops from a generative cell (PO:0020097) or the body cell (PO:0025526) and is part of the pollen (PO:0025281).
Add reference: to Singh 1978- Gymnosperm embryology, Raven 5th edition
- should be: part_of the microgametophyte (PO:0025280)
Notes from previous discussions:
- spermatogenous cells also occur in non-seed plants- (check with Eames)... in ferns as well, so we cannot refer to seed plants alone.
- May need to add new term for pollen sperm cell in angiosperms, which develops from generative cell and pollen sperm cell in gymnos, which develops from pollen spermatogenous cell (or body cell)
- Do we need to differentiate the gymno pollen from the angiosperm pollen?
Other new terms that we should probably add with definitions derived from Singh and Raven:
- prothallial cell- part of the gymnosperm pollen grain
Definition from Raven 5th ed: The sterile cell or cells found in the male gametophytes, or microgametophytes of vascular plants other than angiosperms; believed to be the remnants of the vegetative tissue of the male gametophyte.
Singh: The sterile cell cut off by the microspore and the central cell. Formed by the
- central cell- could be called microspore central cell, to avoid confusion
- stalk cell (of sterile cell)
- antheridial inital
- antheridial cell
- tube cell
- male gametes
Existing terms:
- plant sperm cell (PO:0000084)
- microspore (PO:0020048)
Upcoming meetings and Presentations 2012-2013:
PAG 2013, San Diego, CA; January 12th - 16th, 2013
We will be running a workshop focusing on:
Applications of Ontologies for Plant and Animal Genomics
- Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6
Speakers: Eva Huala, Reinhard Simon, Elizabeth Arnaud, Chris Mungall, and Pankal will present the cROP Vision
JP will be presenting a SIA Computer Demo:
Date and Time: Sunday, January 13, 2013; 5:20 PM, California room
Biocuration 2013 conference, Cambridge, 7-10th April 2013
submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.
possible venue for cROP white paper?
website and registration are now open: Biocuration 2013
PRO-PO-GO meeting, May 15-16th 2013
Please see this page for more information: PRO-PO-GO_Meeting
Location: Buffalo, NY
Dates: May 15-16th, 2013.
Goals:
- To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
- To identify potentially fruitful applications which such enhanced coordination might bring
- To enhance the Protein Ontology treatment of plant-related proteins
- To address coordination issues between the GO and PO, for example as concerns treatment of development stages
- To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]
Tentative participant list:
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)
BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO
10th Extended Semantic Web Conference (ESWC) Montpellier, 26-30 May 2013
Extended Semantic Web Conference Montpellier
Location: Montpellier, 26-30 May 2013.
Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.
Paraphrased from email exchange with EA (Bioversity):
"We are finalizing a workshop proposal to be submitted in the 23rd to the conference organizing committee. In parallel, we are developing a proposal for raising some support funds.
Ontologies will be part of the workshop discussion. The latest development sent by Justin on AISO also raised interest of the organizing committee. So, we would you like that the Plant Ontology team be represented in the scientific committee of our workshop.
This is a very first draft of course but will provide you with the context, scientific objectives, and expected outputs. Would you accept in principle (if the workshop is accepted and funds raised) to join our committee and submit a a paper for a presentation and/or poster? Deadline will be March and April.
MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013
5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)
The New York Botanical Garden & Fordham University
