POC Conf. Call 11-20-12
POC meeting, Webex Conference Call; Date: Tuesday Nov 20th, 2012 10am PST/1pm EST
In attendance:
POC members:
Absent:
Collaborators:
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.
PJ will be out last week of Nov, till Dec 2nd.
Update from Cornell:
MAG: We have photographed 22 new slides (total 379 images)
-Update of schedule:
- In the field from December 1 to Jan 5th, no email access
- In New Zealand from January 17th to Feb 1st (no or very limited access after Jan 15th)
From POC_Conf._Call_10-16-12: PJ will work with MAG to create a mirror of the image database at OSU in early November. Images are ready to share at any time.
MAG has been adding key words to the images and RW adds PO ids where appropriate.
Any news?
phloem terms
Bob Turgeon sent comments on the definitions for companion cells.
From POC_Conf._Call_10-16-12: RW will add his comments to the SF tracker item.
Asked MAG to send the information to LC.
Update from NYBG
Is there a plan for hiring a new curator to fill Ramona's vacated position?
Wrapping up some open trackers: from Items_for_future_meetings page
archegonium egg cell
current def'ns:
archegonium egg cell (PO:0025122): A plant egg cell that is produced by and located in an archegonium.
archegonium (PO:0025126): A plant gametangium that produces an archegonium egg cell that is located in it.
proposed revised def'n: archegonium (PO:0025126): A plant gametangium (PO:0025124) that produces and contains an archegonium egg cell (PO:0025122).
plant gametangium (PO:0025124): A plant organ that produces one or more gametes that are located in it and is part of a whole plant in the gametophytic phase.
proposed revised def'n: A plant organ (PO:ID) that produces and contains one or more gametes (PO:0025006) that are located in it and is part of a whole plant (PO:ID) in the gametophytic phase(PO:ID).
Link to SF for archegonium
Tuber
Currently: tuber: PO:0004543: A shoot axis (PO:0025029) that is radially enlarged and develops from a branch (PO:0025073)
proposed: A plant axis (PO:0025004) that is radially enlarged and develops from a branch (PO:0025073) or a root (POID).
Synonyms: need to tweak
narrow: shoot axis branch tuber, exact: tuber branch
broad: diaspore
Comment: Functions in storage of photosynthate metabolites. This term should be used for tubers derived from branches, as found in Solanum spp. (e.g. potato) or Dioscorea spp. (e.g. yam) and other species. Use the term tuberous root (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis.
Propose new child term:
Shoot axis tuber (new POID): A shoot axis (PO:0025029) that is radially enlarged and develops from a branch (PO:0025073)
root tuber
Currently: We have PO:0025476 tuberous root: A radially enlarged root (PO:0009005).
Propose new term: tuberous root: A root (PO:0009005) that is radially enlarged relative to other lateral or shoot-borne roots on the same plant but not as enlarged as a tuberous root tuber.
comment: A tuberous root, as found in Cassava, may develop through further enlargement into a tuberour root tuber.
proposed rename (PO:0025476): new name: tuberous root tuber: A tuber (PO:0004543) that develops from a tuberous root (PO:0009005)and is further radially enlarged.
add: develops from relationship
Plant Structure Dev Stage terms continued from last meeting:
Upcoming meetings and Presentations 2012-2013:
PAG 2013, San Diego, CA; January 12th - 16th, 2013
- Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6
We will be running a workshop focusing on:
Applications of Ontologies for Plant and Animal Genomics
Speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud, Chris, PJ present the Ref Plant Ontology Vision
- Need to submit the abstracts for the speakers by November 9, 2012.
Deadline for abstracts for computer demos and posters and workshops is Nov 9th
JP will be presenting a SIA computer demo.
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 2013
Please see this page for more information: PRO-PO-GO_Meeting
Location: Buffalo, NY
Tentative Dates: May 8-9th or 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
MONOCOTS V Meeting at NYBG
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
Next meeting scheduled for Tuesday, Nov 20th, 2012 at 10am Pacific/1pm Eastern
Note: no meeting Nov 27th- PJ and LC will both be away
