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

POC_Conf._Call_10-16-12:

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

archegonium egg cell (PO:0025122): A plant egg cell that is produced by and located in an archegonium.

PO:0025126: archegonium: 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).

Link to SF for archegonium

plant gametangium (PO:0025124): 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).

tuber

Currently: tuber: PO:0004543: A shoot axis (PO:0025029) that is radially enlarged and develops from a branch (PO:0025073).

But this cannot be the parent for the tuberous root tubers of species such as Cassava, as they are root-derived. I propose we rename the existing tuber term and make it a sub-class of a new tuber term:

Propose new parent term: tuber: (new PO ID): A plant axis (PO:0025004) that is radially enlarged and develops from a branch (PO:0025073) or a root (PO:0009005).

shoot axis tuber (PO:0004543): A tuber that is a radially enlarged shoot axis (PO:0025029) and develops from a branch (PO:0025073).

This change will only have minor impact on the def'ns on the subterranean tuber terms we have, and we will not have to change their already-long names. And it will actually clarify their origins.

e.g. subterranean tuber (PO:0004547)

Existing def'n: A tuber (PO:0004543) that is below ground.

Revised def'n: A shoot axis tuber (PO:0004543) that is below ground.

e.g. aerial tuber (PO:0004548)

Existing def'n: A tuber that is above ground.

Revised def'n: A shoot axis tuber (PO:0004543) is above ground.

proposed: rename existing tuber term: Shoot axis tuber (PO:0004543): A tuber that is a radially enlarged shoot axis (PO:0025029) and develops from a branch (PO:0025073)

Synonyms and comment: move to 'shoot axis tuber' (PO:0004543)

narrow: shoot axis branch tuber, exact: tuber branch; broad: diaspore

Existing 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 tuber (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis. see below:

tuberous root tuber

Currently: We have tuberous root (PO:0025476): A radially enlarged root (PO:0009005).

existing: Comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuber root may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuber roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuber root is attached. A tuber root usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).

Propose new term: tuberous root (new PO:ID): A root (PO:0009005) that is radially enlarged relative to other lateral roots (PO:0020121) or shoot-borne roots (PO:0000042) on the same plant but not as enlarged as a tuberous root tuber (new PO:ID).

comment: A tuberous root, as found in Cassava, may develop through further enlargement into a tuberous root tuber (PO:0025476).

proposed new name: tuberous root tuber: (PO:0025476): A tuber (PO:0004543) that develops from a tuberous root (new PO:ID) and is further radially enlarged.

add: develops_from relationship

Revised comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams.

• Use the terms shoot axis tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches.
• A tuberous root tuber (PO:0025476) may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants.
• Sometimes tuberous roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuberous root is attached.
• A tuberous root usually develops from a shoot-born root (PO:0000042) or a lateral root (PO:0020121).

Add "root tuber" and "tuber root" as exact synonym.

background notes:

On further investigation, it seems that not only primary growth is involved in the formation of root tubers. There is secondary thickening from irregular growth from the vascular cambium, as well as thickening due to cell division in the cortex. Need to look into it more.

Also, it seems there are both tuberous roots (enlarged roots that form tubers along part of their length), and tubers, that form within those roots (see http://aob.oxfordjournals.org/content/38/2/307.full.pdf+html and hortsci.ashspublications.org/content/44/3/651.full.pdf)

Plant Structure Dev Stage terms continued from last meeting:

items will be moved here from Items_for_future_meetings page

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

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:

1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
2. To identify potentially fruitful applications which such enhanced coordination might bring
3. To enhance the Protein Ontology treatment of plant-related proteins
4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
5. 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

MONOCOTS V:

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, Dec 4th, 2012 at 10am Pacific/1pm Eastern

Note: no meeting Nov 27th- PJ and LC will both be away