POC Conf. Call 11-20-12

POC meeting, Webex Conference Call; Date: Tuesday Nov 20th, 2012 10am PST/1pm EST

In attendance:

POC members: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Dennis W Stevenson (NYBG)

Absent: Ramona Walls (NYBG), Chris Mungall (LBLL)

Collaborators: None

AISO Announcement- note name change

The Plant Ontology Consortium is pleased to announce a new desktop application: AISO (Annotation of Image Segments with Ontologies), v0.2.1 beta.

Download the most recent version of AISO (including installation instructions) here: AISO v0.2.1.

Currently available on Linux and Mac OS X (64-bit). A Windows-compatible version is undergoing testing.

Requesting Features and Reporting Problems: If you have an additional feature you would like to suggest, or if you have encountered any issues while using AISO, please send us an email at <aiso-support@plantontology.org>.

You may also monitor our Jaiswal Lab Software page for AISO updates.

MAG's technician has already installed AISO and is using it to annotate the images.

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) and we have added 4 more slides (235 photos total from last week).

-Update of schedule:

• In the field from December 1st to Jan 5th, no email access (some access on Dec 2,3rd)
• 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.

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.

MAG sent the information to LC, who will post it on the above tracker.

Updates and Progress Reports Needed for Annual Report

• Need 1 to 1.5 page of progress report for the last year. Address the concerns that NSF had last year- how they were addressed.
• Need a report on the budgets- how much is un-expended by end of Dec 2012 and Feb 15th 2013, and how you plan on spending it.
• Not on existing deliverable, but new work for the no-cost extension

Update from NYBG

Is there a plan for hiring a new curator to fill Ramona's vacated position?

• NYBG has about 1 year salary for replacement position, would like to have it filled for the beginning of the new year.
• Would like to add to the imaging efforts from the NYBG collections
• Will send PJ the advertisement and it can be posted on the web page and at the BSA, etc

Wrapping up some open trackers: from Items_for_future_meetings page

archegonium egg cell

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

proposed revised def'n: archegonium egg cell (PO:0025122): A plant egg cell (PO:0020094) that develops from the archegonium central cell (PO:0025509) and is contained in the archegonium (PO:0025126).

Comment: The archegonium central cell divides asymmetrically to form a smaller archegonium neck canal cell (PO:0030065) and a larger archegonium egg cell (PO:0025122) in gymnosperms.

• 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 develops from an archegonium initial cell (PO:0025510) and has as parts a venter (PO:0030038),and an archegonium neck (PO:0030039).

proposed comment: At maturity, the archegonium contains an archegonium egg cell (PO:0025122). In mosses, the archegonium also has part an archegonium stalk (PO:0030036).

DWS: The archegonium is a multicellular structure; has a number of components: the neck, the archegonium neck cell; central canal cell, as well as the archegonium egg cell. It is essential to include these in definition, it will eliminate the circularity.

PJ: We should not say: 'produced by', it is better to say that the archegonium egg cell develops_from a specific cell type in the archegonium,

The archegonium egg cell develops_from the archegonium central cell, it has a common origin with the central canal cell.

DWS: The archegonium is a female gametangium composed of neck cell, neck canal cells, a ventral canal cell and the archegonial egg cell. - common to all bryophytes, gymnosperms and ferns.

• archegonium central cell (PO:0025509): A plant cell (PO:0009002) that is the distal cell arising from the first division of an archegonial initial cell (PO:0025510) in a gymnosperm.

Comment: The archegonium central cell is larger than the other cell that arises from the initial division of the archegonium initial cell. Divides asymmetrically to form a smaller archegonium neck canal cell (PO:0030065) and a larger archegonium egg cell (PO:0025122) in gymnosperms.

Currently: 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).

need to open separate tracker for plant gametangium, currently included with archegonium'

• archegonium initial cell (PO:0025510): An initial cell that is part of an archegonium megagametophyte (PO:0025282) and divides to give rise to an archegonium (PO:0025126).

should have a part_of relation to archegonium megagametophyte (PO:0025282); probabaly need to reword this def'n as well.

Part_of children of archegonium: We currently have:

• archegonium stalk (PO:0030036): A stalk that the basal part of an archegonium. Comment: Raises the venter above the rest of the gametophyte.

revised def'n: A stalk that is the basal part of an archegonium which raises the venter above the rest of the gametophyte.

• archegonium neck (PO:0030039): A cardinal organ part that is the elongated apical part of an archegonium. Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

• venter (PO:0030038): A cardinal organ part that is the enlarged basal part of an archegonium and has an archegonium egg cell located in it.

• archegonium neck canal (PO:0030066): A canal in the center of an archegonium neck. Comment: Forms after the archegonium neck canal cells disintegrate.

• archegonium neck canal cell (PO:0030065): A plant cell that is one of the axial row of cells in an immature archegonium neck. Comment: As the archegonium matures, the archegonium neck canal cells disintegrate to form the archegonium neck canal.

central cell (PO:0020090): The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.

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).

DWS: Suggest to leave off the last phrase: and just define it as: tuber: (new PO ID): A plant axis (PO:0025004) that is radially enlarged.'

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

Propose revised definition: shoot axis tuber (PO:0004543): A tuber (PO:0025522) that develops from a branch (PO:0025073).

We do not need to repeat that it is a radially enlarged shoot axis (PO:0025029), since that is part of the parent definition.

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

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

need to check on 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.

modified: Use the term tuberous root tuber (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis. see below:

---

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) develops 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) develops above ground.

PJ: Perhaps you need two types of subterranean tubers? For the shoot axis tuber and the tuberous root tubers?

Part_of children of tuber: these will need to be dealt with:

• PO:0025068 : tuber axillary bud meristem
• PO:0025040 : tuber axillary vegetative bud
• PO:0025046 : tuber epidermis
• PO:0025043 : tuber periderm
• PO:0025036 : tuber storage parenchyma

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).

new term: tuberous root (PO:0025523): 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 (PO:0025476)

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).

Should remove "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." from the comment.

• Sometimes tuberous roots bear vegetative buds (PO:0000058) from adventitious buds.

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)

LOWE SB, WILSON LA (1974) Comparative Analysis of Tuber Development in Six Sweet Potato (Ipomoea batatas (L.) Lam) Cultivars: 1. Tuber initiation, tuber growth and partition of assimilate. Annals of Botany 38: 307–317

generative cell (PO:0020097) and related terms

generative cell (PO:0020097) and related terms

We need to fix this definition, as it currently only includes angiosperms:

propose change (PO:0020097) to a spermatogenous cell and make generative cell a synonym of it

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]

Proposed new name def'n: spermatogenous cell (PO:0020097): A plant cell (PO:0009002) of the microgametophyte (PO:0025280) (of seed plants) that divides to produce two plant sperm cells (PO:0000084).

Exact synonymns: generative cell, body cell

Add reference: to Singh 1978- Gymno embryology

Note that spermatogenous cells also occur in non-seed plants- (check with Eames)... in ferns as well, so we cannot refer to seed plants alone. definition- what

should be: part_of the microgametophyte (PO:0025280)

suggest making it part_of pollen (PO:0025281) -- only found in seed plants

Definition 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

proposed definition: spermatogenous cell: raven: the cell of the male gametophyte or pollen grain of gymnosperms, which divides to form 2 sperm cells

Probably should also have the 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.

Generative cells can occur in both angiosperms and gymnosperms. They are the same thing, even though they develop into something else. Need to look at Singh's book on gymnosperm embryology.

Existing:

plant sperm cell (PO:0000084)

---

From Pankaj:

Please add the following anatomy term required for the rice gene expression data I am annotating http://www.ncbi.nlm.nih.gov/pubmed/22046259

PO:0020097 : generative cell

--IS_A--pollen generative cell (NEW-suggested)<--[ please add]

--DEVELOPS_FROM-- PO:0025121 : pollen sperm cell [please add this relationship]

Generative cell is not found outside pollen-bearing plants. Suggest just adding this term as a synonym. Special class would be redundant, as there is no non-pollen generative cell.

Agree to add pollen sperm cell develops_from generative cell. BUT only in angiosperms

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.

We need these synonyms:

• body cell (of generative cell)

• central cell
• prothallial cell
• stalk cell (of sterile cell)
• antheridial inital
• antheridial cell
• tube cell
• male gametes

have:

• microspore (PO:0020048)

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