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

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'''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_3-15-11]]?
+
''There were no changes, additions, or deletions.''
  
==Issues from last week's meeting:==
 
  
==Continuing User requests: for PSO==
+
=Issues arising from last week's meeting:=
  
- Deal with and complete the list of user requests on SourceForge-
+
Special technical meeting?
  
===[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]===
+
''The conference call will take place on 3-17-11, at 4PM PDT.''
  
submitted by Austin Mast
+
''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]].''
  
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
+
=Physcomitrella terms=
  
[https://sourceforge.net/tracker/?func=detail&aid=3165981&group_id=76834&atid=835555 fascicle] The term fascicle can refer to different structures in different taxa. Suggest we use the term '''floral fascicle''' or '''flower fascicle''' in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
+
''Discussion of new terms was postponed until next week, due to low attendance.''
  
From Tucker, 2003, Flora:
+
==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium and related terms]==
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
 
that two to several flowers are initiated in each bract axil rather than
 
just one as in a raceme. '''The cluster of flowers at each node is called a fascicle.''' The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows
 
'''the fascicle to be a short shoot topped by a second order inflorescence apical meristem'''. This meristem initiates
 
flowers in a bilaterally symmetrical order: a single abaxial flower, then
 
two lateral flowers, another median abaxial, then two more laterals. The
 
number of flowers per fascicle depends on the duration of the axillary
 
inflorescence apex of the short shoot, which ceases activity after
 
initiating the few flowers in the fascicle. No flowers are initiated
 
adaxially (toward the first order axis) on the short shoot (Tucker, 1987b;
 
Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be
 
distinguished from a cyme in that every flower is bract subtended in a
 
pseudoraceme."
 
  
Suggested def: A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated.  Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
+
==apical cell==
  
 +
==Collective plant structures:==
  
[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle] (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
==Plant organs:==
  
We added the term stipule spine. Could also add the term '''stipule bristles''': A stipule that has a brush-like appearance.
+
==Additional moss terms:==
  
Alternative is to suggest bristled to PATO
+
==Cardinal organ parts==
  
 +
''See [[POC_Conf._Call_3-22-11]] for details.''
  
[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode] Suggested def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
+
=Upcoming meetings 2011:=
 +
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
 +
[http://icbo.buffalo.edu ICBO]
  
[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]
+
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.
  
'''Banner''' (as in a legume flower) - suggest using name 'banner petal'
+
'''Full-Day Workshops Schedule:'''
  
Suggested def: A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
+
'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
 +
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
'''Wing''' (as in a legume flower) - suggest using name 'wing petal'
+
'''July 26 6.30pm-9pm''' Evening Workshop: Common Logic
  
Suggested def: One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.
+
'''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).
  
'''Keel''' (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name 'corolla keel'
 
  
Suggest three new terms:
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
fused petal: A petal that is fused to another petal. Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
fused corolla: A corolla in which the petals are fused. Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
corolla keel: A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae. Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.  
+
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'''.
  
[https://sourceforge.net/tracker/?func=detail&aid=3166008&group_id=76834&atid=835555 locule] The term locule can be used to refer to the cavity in an carpel or in an anther.  In the PGDSO, we have the term PO:0001026 locules established, which is an anther development stage. For clarity, we may want to add two terms: locule, anther locule and carpel locule.
+
TAIR is organizing an Outreach Booth and we are invited to take part.
  
anther locule: A plant anatomical space that is a cavity in an anther formed by a single pollen sac.
 
  
carpel locule: A plant anatomical space that is a cavity in a carpel that contains at least one ovule. Comment: A syncarpous gynoecium may have multiple locules, and the locules of multiple carpels may be fused.
+
'''* International Botanical Congress (IBC2011)'''
  
May want to add general parent terms locule: A plant anatomical space that is a cavity within a sporophyll. Synonym: loculus
+
July 23rd-30th 2011, Melbourne, Australia'''
 +
 
 +
Registration is open  [http://www.ibc2011.com/Dates.htm 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==

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