Difference between revisions of "POC Conf. Call 3-15-11"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(29 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
'''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)'''
 
'''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)'''
  
In attendance:  
+
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG),  Justin Elser (OSU), Justin Preece (OSU)
  
POC members:
+
Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
  
Absent:
 
 
Collaborators:
 
  
 +
Collaborators: none
  
 
Acceptance of the minutes from the [[POC_Conf._Call_3-8-11]]?
 
Acceptance of the minutes from the [[POC_Conf._Call_3-8-11]]?
  
=Issues arising from last week's meeting:=
+
''There were no changes, additions, or deletions.''
 
 
=Physcomitrella terms=
 
  
==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium]==
 
  
May want to use the name '''plant gametangium''', to make it clear that we are not including algae.
+
=Issues arising from last week's meeting:=
  
Proposed definitions:
+
Special technical meeting?
  
Plant gametangium: A cardinal organ part (?) that is part of a whole plant in the gametophytic phase and produces gametes.
+
''The conference call will take place on 3-17-11, at 4PM PDT.''
  
(need to distinguish this from embryo sac somehow)
+
''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it.  Will post possible alternative solutions on the [[POC Technical Issues Page]].''
  
Antheridium: A gametangium that produces antheridium sperm cells.
+
=Physcomitrella terms=
  
Archegonium: A gametangium that produces archegonium egg cells.
+
''Discussion of new terms was postponed until next week, due to low attendance.''
  
We also have the terms:
+
==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium and related terms]==
 
 
archegonium egg cell (PO:0025122): An egg cell that is produced by an archegonium.
 
 
 
embryo sac egg cell (PO:0025123): An egg cell that is produced by a megagametophyte.
 
  
 
==apical cell==
 
==apical cell==
 
Moss Ontology has requested the term '''apical cell'''.
 
 
We already have the term '''apical cell (PO:0004000)''', which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." Suggest renaming PO:0004000 "embryonic apical cell" for clarity. The embryonic apical cell can also be found in non-angiosperms.
 
 
Growth in mosses (and other bryophytes and ferns) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. The moss apical meristem may differ from that of vascular plants, but it is still possible to call it an apical meristem.
 
 
Apical cell is consistent with the definition of meristematic cell (synthesizing protoplasm and producing new cells by division and with only a primary cell wall). Meristematic cell is part_of meristem, and a meristem is a portion of tissue and therefore two or more cells. We do not need to add apical cell part of apical meristem, but logically it will be part of a meristem.
 
 
'''Proposed def. of apical cell:''' A meristematic cell at the apex of a gametophore or non-vascular leaf (phyllid).
 
 
Comment: Occurs in mosses and other bryophytes. Does it also occur in ferns? Need to read up on this.
 
  
 
==Collective plant structures:==
 
==Collective plant structures:==
 
===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore]===
 
 
Def'n supplied by Moss Ontology: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.
 
 
Suggest is_a shoot system.
 
 
Proposed def'n.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase
 
 
Comment: A gametophore is the leafy part of a moss gametophyte, without the protonema. Antheridia and archegonia arise on the gametophore.
 
 
===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud]===
 
 
The term "bud" has been requested:
 
Def'n supplied by Moss Ontology: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove
 
 
Suggest a new term '''gametophore bud'''. This could be a child of bud (PO:0000055: An undeveloped shoot system).
 
 
Proposed def'n: A bud on a protonema that develops into a gametophore. participates_in gametophytic phase
 
 
Comment: Occurs in mosses.
 
  
 
==Plant organs:==
 
==Plant organs:==
 
===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]===
 
- This is the term used for the gametophore stem or axis.
 
 
Suggest using '''gametophore axis''' as primary name, cauloid as synonym.
 
 
Proposed def'n: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase
 
 
Synonyms: cauloid, gametophyte axis
 
 
Also suggest adding terms for '''gametophore stem''' and '''gametophore branch''' (similar to stem and branch).
 
 
 
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract]===
 
 
- The specialized phyllids surrounding the antheridia.
 
 
Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
 
 
A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.
 
 
Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase
 
 
Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.
 
 
  
 
==Additional moss terms:==
 
==Additional moss terms:==
  
These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we may as well add them now.
+
==Cardinal organ parts==
  
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perichaetal bract]===
+
''See [[POC_Conf._Call_3-22-11]] for details.''
  
Proposed def'n: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.
+
=Upcoming meetings 2011:=
 +
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts.  The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.
+
[http://icbo.buffalo.edu ICBO]
  
===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth]===
+
LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
 +
Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted)
 +
LC is working with the other organizers to develop the workshop plans and a call for papers.
  
Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on an axis that are fused laterally and surround the calyptra.
+
'''Full-Day Workshops Schedule:'''
  
Should it be surrounds the capsule, in case no calyptra is present?
+
'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
-has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
===[https://sourceforge.net/tracker/?func=detail&aid=3185175&group_id=76834&atid=835555 seta]===
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
-The stalk of a moss sporophyte.
 
  
Suggested def'n: A plant axis that that holds up a spore capsule. participates_in sporophytic phase
+
- LC will attend and represent the PO, will submit a short paper/poster for the workshop (deadline April 1st).
  
==Cardinal organ parts==
 
Terms requested by MO:
 
  
calyptra
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
base
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
peristome
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
theca
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
lid
+
Abstract deadlines: Your abstract must be submitted by '''March 11''' if you want it to be considered for a minisymposium talk.
  
foot
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
neck canal
+
TAIR is organizing an Outreach Booth and we are invited to take part. 
  
  
Other terms, not from MO
+
'''* International Botanical Congress (IBC2011)'''
  
epiphram
+
July 23rd-30th 2011, Melbourne, Australia'''
  
spore capsule mouth
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
pseudopodium
+
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.
  
venter
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
  
=Upcoming meetings 2011:=
+
Early bird registration deadline - Extended 1 March 2011
 +
Deadline for registration by presenters 1 March 2011
  
 +
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
  
  
 
==Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PDT==
 
==Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PDT==

Latest revision as of 21:00, 21 March 2011

POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU)

Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)


Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_3-8-11?

There were no changes, additions, or deletions.


Issues arising from last week's meeting:

Special technical meeting?

The conference call will take place on 3-17-11, at 4PM PDT.

RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it. Will post possible alternative solutions on the POC Technical Issues Page.

Physcomitrella terms

Discussion of new terms was postponed until next week, due to low attendance.

Gametangium, antheridium, archegonium and related terms

apical cell

Collective plant structures:

Plant organs:

Additional moss terms:

Cardinal organ parts

See POC_Conf._Call_3-22-11 for details.

Upcoming meetings 2011:

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted) LC is working with the other organizers to develop the workshop plans and a call for papers.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO, will submit a short paper/poster for the workshop (deadline April 1st).


*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

TAIR is organizing an Outreach Booth and we are invited to take part.


* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

Early bird registration deadline - Extended 1 March 2011 Deadline for registration by presenters 1 March 2011

See IBC 2011 Bio-Ontologies Symposium wiki page for more details


Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PDT