POC Conf. Call 12-11-12

POC meeting, Webex Conference Call; Date: Tuesday Dec 11th, 2012 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Barry Smith (University at Buffalo, NY),, Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU)

Absent: Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Ramona Walls (NYBG), Chris Mungall (LBLL)

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=70633842&rKey=a09f138806f380c5

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=70633842&rKey=370f612ea2b73f8f

Plans for Upcoming Release #19

Timeline for Release: Goal is mid December 2012 Release_19

Priorities for inclusion in the Release:

- Revisions to PSDS: including Fruit development stages

- Cleaning up some of the open trackers for the PAE branch

- New datasets: grape, cotton, rice

- LC has been working with YY and JE to update the Japanese translations- in the next release, we anticipate these will be displayed on the live site.

Updated Goal: is to complete the edits and annotation sets by end of the day Friday Dec 14th, then start loading the database onto beta. That will give us the beginning of next week to troubleshoot issues and hopefully have it completed by Dec 18th.

Will check with the collaborators if there are any new annotations and also check with RW, if there things that need to be fixed

Open trackers: To be fixed:

generative cell (PO:0020097) and related terms

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:

Proposed 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).

body cell (new; PO:0025525): A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280) in gymnosperms, that divides to produce the ' sterile cell and the pollen sperm cell (PO:0025121).

add broad synonym: gymnosperm generative cell

If it is true that ALL angiosperms produce two pollen sperm cells, then we do not need to say "in angiosperms". Can put that into the comment. Are there any gymnosperms where the spermatogenous cell divides to produce two pollen sperm cells?

See reference from PJ: Rudall and Bateman

'Revised def'n: generative cell (PO:0020097): A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280) that divides to produce two pollen sperm cells (PO:0025121).

Revised def'n: body cell (PO:0025525): A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280), that divides to produce the 'vegetative cell and pollen sperm cells (PO:0025121).

Could possibly come up with a better name for this term. Add comment- occurs in gymnosperms. Prefer vegetative cell over 'sterile 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).

Just say a "pollen sperm cell (PO:0025121): A plant sperm cell (PO:0000084) that is part of the pollen (PO:0025281)." With comment: angiosperm pollen sperm cell arises from the generative cell and gymnosperm pollen sperm cells arise from body cells. You do not need to have the deelops from in the definition.

Revised def'n: pollen sperm cell (PO:0025121) as: A plant sperm cell (PO:0000084) that is part of the pollen (PO:0025281).

Revised comment: In angiosperms, the pollen sperm cell arises from the generative cell (PO:0020097). It gymnosperms, the pollen sperm cell arises from the body cell (PO:0025525).

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? not right now, the solution above was accepted

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.

the prothallial cell is present in all the other plants but the angiosperms

• central cell- could be called 'microspore central cell', to avoid confusion

• stalk cell (of sterile cell)- need to clarify what this is

• antheridial inital and antheridial cell: need a different name for both of these

• tube cell - pollen tube cell PO:0025195

• male gametes- plant sperm cell (PO:0000084)

Existing terms:

• pollen tube cell PO:0025195

• plant sperm cell (PO:0000084)

• microspore (PO:0020048)

archegonium and associated parts:

archegonium (PO:0025126)

Revised def'n: A multicellular 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).

Revised comment: At maturity, the archegonium produces an archegonium egg cell (PO:0025122). In mosses, the archegonium also has part an archegonium stalk (PO:0030036). The archegonium (PO:0025126) occurs in bryophytes and pteridophytes, but never in angiosperms, where the female gamete (plant egg cell; PO:0020094) is produced by the embryo sac (PO:0025074), a specialized (reduced) gametangium.

Plants:Diversity and Evolution- Ingrouille and Eddie(2006) ISBN-10: 0521794331,ISBN-13: 9780521794336

Accepted, closing this tracker.

archegonium initial cell

Existing (new):

archegonium initial cell (PO:0025510): An initial cell (PO:0004011) that is part of the archegonium megagametophyte (PO:0025282), and which divides asymmetrically to form an archegonium central cell (PO:0025509) and a smaller archegonium neck canal cell (PO:0030035).

relations:

• archegonium initial cell (PO:0025510) part_of archegonium megagametophyte (PO:0025282)
• archegonium central cell (PO:0025509) develops_from archegonium initial cell (PO:0025510)
• archegonium neck canal cell (PO:0030035) develops_from archegonium initial cell (PO:0025510)

from Rudall, 2006: "In gymnosperms such as Ephedera, each archegonial initial undergoes an asymmetric mitosis to form a large central cell and a smaller neck cell."

Question: Does the archegonium always exist as part of the archegonium megagametophyte, and does the archegonium megagametophyte always have as part an archegomnium? What about in bryophytes and pteridophytes?

archegonium central cell

archegonium central cell (PO:0025509): A plant cell (PO:0009002) that is the larger, distal cell arising from the first division of an archegonium initial cell (PO:0025510).

Comment: The archegonium central cell divides asymmetrically to form a smaller ventral canal cell (PO:0025524) and a larger archegonium egg cell (PO:0025122). It is larger than the archegonium neck canal cell (PO:0030065), which also develops from the archegonium initial cell (PO:0025510). The archegonium central cell only occurs in gymnosperms.

Reference rudall paper: PMID_17041880

Is this true: The archegonium central cell only occurs in gymnosperms. Note from Skype discussion: MG: In ferns they do not use the term 'central cell'- use ventral canal cell.

embryo sac central cell

embryo sac 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.

only in angiosperms

venter (PO:0030038)

venter (PO:0030038):

Revised def'n: A cardinal organ part (PO:0025001) that is the enlarged basal part of an archegonium (PO:0025126) and has an archegonium egg cell (PO:0025122) located in it.

moved the relation "archegonium egg cell located_in venter" rather than "archegonium egg cell located_in archegonium". Is this true for all?

from wikipedia:

"In bryophytes, the calyptra (plural calyptrae) is an enlarged archegonial venter that protects the capsule containing the embryonic sporophyte.[1] The calyptra is usually lost before the spores are released from the capsule. The shape of the calyptra can be used for identification purposes.[2]"

1. Ralf Reski (1998): Development, genetics and molecular biology of mosses. In: Botanica Acta. 111, 1-15.
2. Malcolm; Malcolm, Bill; Nancy (2006), Mosses and other Bryophytes, an Illustrated Glossary, Micro-Optics Press, p. 65, ISBN 0-9582224-7-9

We decided to to define the calyptra as arising from the archegonium. Will add synonym; archegonium base

spore capsule calyptra

spore capsule calyptra (PO:0030037):

Current def'n: A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.

Proposed definition: A cardinal organ part (PO:0025001) that develops from an archegonium venter (PO:0030038) and is a cap or hood enclosing the sporangium (syn: spore capsule; PO:0025094).

Proposed comment: Found in bryophytes. The spore capsule calyptra is a membranous or hairy cap or hood, composed of gametophytic tissue (venter; PO:0030038) that protects the embryonic sporophyte within the archegonium (PO:0025126). In some species, it may persist after the sporophyte develops and gets carried upward as the seta (PO:0030032) elongates. The spore capsule calyptra is usually lost before the spores are released, and its shape can be used for identification purposes.

We decided to stay with the existing definition, making the origin of the spore capsule calyptra more vaguely defined as arising from the archegonium.

Current def'n (on live): A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.

Revised def'n: A cardinal organ part (PO:0025001) that develops from an archegonium (PO:0025126) and is a cap or hood enclosing the sporangium (syn: spore capsule; PO:0025094).

Proposed comment: Found in bryophytes. The spore capsule calyptra is a membranous or hairy cap or hood, composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium (PO:0025126). In some species, it may persist after the sporophyte develops and gets carried upward as the seta (PO:0030032) elongates. The spore capsule calyptra is usually lost before the spores are released, and its shape can be used for identification purposes.

archegonium neck (PO:0030039)

Added PO IDs:

archegonium neck (PO:0030039): A cardinal organ part (PO:0025001) that is the elongated, apical part of an archegonium (PO:0025126).

Comment: At maturity, the neck canal cells (PO:0030065) and the ventral canal cell (PO:0025524) disintegrate, creating a archegonium neck canal (PO:0030066) for the plant sperm cells (PO:0000084) to enter the archegonium (PO:0025126).

Add venter neck as a broad synonym

• archegonium neck canal (PO:0030066):

A canal (PO:0025132) in the center of an archegonium neck (PO:0030039).

Comment: During archegonium development, the archegonium neck canal cells (PO:0030065) and the ventral canal cell (PO:0025524) disintegrate, creating a archegonium neck canal for the plant sperm cells (PO:0000084) to enter the archegonium (PO:0025126).

• archegonium neck canal cell (PO:0030065):

A plant cell (PO:0009002) that is one of the axial row of cells in an immature archegonium neck (PO:0030039).

New term: ventral canal cell:

proposed def'n: ventral canal cell (PO:0025524): A plant cell (PO:0009002) that develops from the archegonium central cell (PO:0025509) and lies at the base of the archegonium neck (PO:0030039), above the archegonium egg cell (PO:0025122) in the venter (PO:0030038).

proposed comment: The ventral canal cell is smaller than the archegonium egg cell (PO:0025122), which also develops from the asymmetric division of the archegonium central cell (PO:0025509). It lack a plant-type cell wall (GO:0009505) (ref?). When the archegonium (PO:0025126) is mature, the ventral canal cell (along with the archegonium neck canal cells; PO:0030065), contributes to the formation of the archegonium neck canal (PO:0030066) by distintegrating and becoming mucilaginous. The canal cells and may produce chemicals to attract the male gametes.

Relations:

• ventral canal cell (PO:0025524) part_of the venter (PO:0030038)
• ventral canal cell (PO:0025524) develops_from archegonium central cell (PO:0025509)

References:

• Ingrouille M, Eddie B (2006) Plants: Diversity and Evolution. Cambridge University Press
• Rudall PJ (2006) How many nuclei make an embryo sac in flowering plants? BioEssays 28: 1067–1071

archegonium stalk (PO:0030036)

Revised def'n: A stalk (PO:0025066) that the most basal part of an archegonium (PO:0025126).

Comment: Raises the venter (PO:0030038) above the rest of the gametophyte.

archegonium egg cell

Revised def'n: A plant egg cell (PO:0020094) that develops from the archegonium central cell (PO:0025509) and is located 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.

Notes: The archegonium egg cell develops_from the archegonium central cell, it has a common origin with the neck canal cell, in ferns they do not use the term 'central cell'- ventral canal cell.

antheridium and associated parts:

Current def'n: antheridium (PO:0025125): A plant gametangium that produces antheridium sperm cells that are located in it. [source: POC:curators]

Comment: An antheridium has a sterile jacket layer that does not produce sperm cells.

Revised def'n: A multicellular plant gametangium (PO:0025124) that produces antheridium sperm cells (PO:0025120)and has as parts an antheridium jacket layer (PO:0030053) and an antheridium stalk (PO:0030035).

Revised comment: An antheridium has a sterile jacket layer (PO:0030052). In both gymnosperms and angiosperms, the antheridium (PO:0025125) is replaced by pollen (PO:0025281).

Structures associated with the antheridium:

Added PO IDs

antheridium jacket layer (PO:0030053): A portion of plant tissue (PO:0009007) that is a single layer of cells on the outside of an antheridium (PO:0025125).

Revised comment: Cells in the antheridium jacket layer surround the inner spermatogenous cells (new PO ID) and do not give rise to antheridium sperm cells (PO:0025120).

antheridium jacket layer cell (PO:0030052): A plant cell (PO:0009002) that is part of an antheridium jacket layer (PO:0030053).

antheridium stalk (PO:0030035): A stalk (PO:0025066) that is the basal part of an antheridium (PO:0025125).

Revised comment: The antheridium stalk raises the antheridium (PO:0025125) from the antheridium head (PO:0030075).

antheridium sperm cell (PO:0025120): A plant sperm cell that is produced by and located in an antheridium.

revised def'n: A plant sperm cell (PO:0000084) that develops from a spermatogenous cell (new PO ID) and is located in an antheridium (PO:0025125).

existing Comment: Antheridial sperm cells are motile and lack a plasma membrane.

Revised comment: Antheridium sperm cells are motile.

remove the relation part_of antheridium, replace with located_in

antheridium head(PO:0030075): A disk-shaped cardinal organ part (PO:0025001) that is the apical portion of an antheridiophore (PO:0030033) and bears antheridia (PO:0025125).

revised comment: Found in mosses and other bryophytes such as the liverwort Marchantiales.

antheridiophore (PO:0030033): A plant axis (PO:0025004) that bears two or more antheridia (PO:0025125) on an antheridium head (PO:0030075).

revised comment: Found in mosses and other bryophytes such as the liverwort Marchantiales.

Rather than saying "bears", it is better to be more specific, and rather than calling it an axis- should be is a stalk.

antheridiophore (PO:0030033) revised def'n: A stalk (PO:0025066) that supports an antheridium head (PO:0030075).

has part antheridium head (PO:0030075)

archegoniophore (PO:0030034): revised def'n: A stalk (PO:0025066) that supports an archegonium head (PO:0030034).

has part archegonium head (PO:0030034)

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 an AISO 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 abstracts for posters is Jan 31st.

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:

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

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):

workshop proposal

"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

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