Difference between revisions of "POC Conf. Call 4-13-10"

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'''1. Complete discussion of whorls:'''
 
'''1. Complete discussion of whorls:'''
  
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a. Proposed new term: '''whorled plant structure:''' proposed definition: A collective plant structure composed of one or more whorls. (See SF Tracker: [http://sourceforge.net/tracker/?func=detail&aid=2982756&group_id=76834&atid=835555/ whorled plant structure]).  
+
a. '''whorled plant structure:''' definition: A collective plant structure composed of one or more whorls. (See SF Tracker: [http://sourceforge.net/tracker/?func=detail&aid=2982756&group_id=76834&atid=835555/ whorled plant structure]).  
 +
 +
''Alejandra, Dennis, and Ramona felt '''strongly''' that 'androecium' and 'gynoecium' were phyllome whorls, along with the agreement of Laurel and Rex.  Laurel discussed this again with Pankaj (after the call) and he agreed that since carpel and stamen are listed as phyllomes, that it makes sense to list androecium and gynoecium as phyllome whorls.  So we all agreed to eliminate the term '''whorled plant structure''', because it was redundant with 'whorled phyllome structure'.''
  
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Children will be phyllome whorled structure, perianth, androecium and  gynoecium.
 
  
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In discussions after the 4-6-10 webex call, PJ suggested this should be called: ''''whorled plant structure'''' and instead of the new term 'whorl', we should keep 'phyllome whorl.  
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b. '''Phyllome whorl:'''(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2980171&group_id=76834&atid=835555/ whorled phyllome structure])
 +
Proposed def'n: "A collective plant structure that contains phyllomes arranged around a common node."
  
 +
''This was renamed as ''''whorled phyllome structure''''.
  
−
*PATO has a term "whorled" (PATO:0001951: A spatial pattern inhering in a bearer by virtue of the bearer's being in opposition round a common axis), so if we use the term "whorled structure," we don't need to include whorl in the PO, but  can cross-ref PATO instead. We will need to rewrite the definition of "whorled plant structure" to reflect the change.
+
''After the meeting Lol and Ramona proposed the new def'n: 'whorled phyllome structure': A collective plant structure that contains one or more whorled arrangements of phyllomes.''
  
−
We discussed structures that can contain multiple whorls, like corolla or perianth, and agreed that by definition, a whorl cannot contain multiple whorls. This structure would encompass these and be a child of collective plant structure.
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''Children are androecium, calyx, corolla, epicalyx, gynoecium, leaf whorl, perianth and whorled tepal structure (new term, see below).''
  
  
 +
Note: Whorls that have been reduced to a single organ will be  placed under 'plant organ'.
  
  
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b. '''Phyllome whorl:'''(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2980171&group_id=76834&atid=835555/ phyllome whorl])
 
−
Proposed new def'n: "A collective plant structure that contains phyllomes arranged around a common node." (minor rewording)
 
−
 
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Child terms:calyx, corolla, epicalyx, leaf whorl, tepal whorl (new term)
 
−
 
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Since all of these children can contain multiple whorls, suggest changing this to '''phyllome whorled structure''': a whorled plant structure that contains two or more phyllomes.
 
−
 
−
Note: Whorls that have been reduced to a single organ will be  placed under 'plant organ'.
 
−
*Remember to add link to the homologous terms. For example, if a flower only contains one carpel, we could add a term like "simple gynoecium" as a child of plant organ with a cross reference to gynoecium.
 
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DWS said this should only be an issue for reproductive parts, since there are no flowers with a single petal. What about sepals?
 
  
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c. Proposed new term: '''tepal whorled structure:''' a whorled structure composed of two (four?) or more tepals. (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2984557&group_id=76834&atid=835555/ whorled tepal structure])  
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''Alejandra, Dennis, and Ramona felt strongly that androecium and gynoecium were phyllome whorls. Created new term '''whorled phyllome structure''', as child of CPS. Did not work on final definition. Eliminated term '''whorled plant structure''', because it was redundant with whorled phyllome structure. Children are androecium, calyx, corolla, epicalyx, gynoecium, leaf whorl, whorled tepal structure (new term, see below).''
 
  
  
 +
''Agreed to rename the term '''whorled tepal structure'''. There was some discussion about whether or not this term should be a child of perianth.''
  
−
c. Proposed new term: '''tepal whorled structure:''' a whorled structure composed of two (four?) or more tepals. (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2984557&group_id=76834&atid=835555/ tepal whorl(ed) structure])
+
''After the meeting Lol and Ramona proposed the new def'n: 'whorled tepal structure': A whorled phyllome structure that is composed of two or more tepals''
  
  
−
''Agreed to add new term '''whorled tepal structure'''. There was some discussion about whether or not this term should be a child of perianth.''
 
  
 +
''Also worked on definition of '''tepal'''(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972262&group_id=76834&atid=835555/ tepal])
  
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''Also worked on definition of '''tepal''': proposed definition: A phyllome that is part of a perianth in which all parts are similar in appearance.''
+
proposed definition: A phyllome that is part of a perianth in which all parts are similar in appearance.''
  
  
 
''There was a discussion about cases in which petals, sepal, or tepals are arranged spirally, rather than in a whorl, as in basal dicots. This creates a problem  for dealing with terms like perianth, which is usually whorled but may be a spiral. No solution was reached.''
 
''There was a discussion about cases in which petals, sepal, or tepals are arranged spirally, rather than in a whorl, as in basal dicots. This creates a problem  for dealing with terms like perianth, which is usually whorled but may be a spiral. No solution was reached.''
  
 +
(See SF Tracker [http://sourceforge.net/tracker/?func=detail&aid=2982629&group_id=76834&atid=835555/ phyllome arrangement])
  
  
−
''Items #2 and #3 were tabld for next week's discussion:''  
+
 
 +
''Items #2 and #3 were tabled for next week's discussion:''  
  
 
'''2. fruit''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972169&group_id=76834&atid=835555/ fruit])  
 
'''2. fruit''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972169&group_id=76834&atid=835555/ fruit])  
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'''4.  Question from Laurel and Ramona about changing the references in OE when we rewrite the definitions of the terms (eg from MaizeGDB/TAIR to POC Curators).  What is the correct protocol for doing this?'''
 
'''4.  Question from Laurel and Ramona about changing the references in OE when we rewrite the definitions of the terms (eg from MaizeGDB/TAIR to POC Curators).  What is the correct protocol for doing this?'''
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''The people present concurred that if we are making a substantial rewrite of the definition, then the Dbxref should be changed to POC: curators.  The ID number shows the historical ''
 
  
 +
''The people present concurred that if we are making a substantial rewrite of the definition, then the Dbxref should be changed to POC: curators.  The ID number shows the history of who created the term.''
 +
After the call, Pankaj pointed out that a substantial change in the definition would require a new ID#.
  
  
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6)  Applications of the CL (Cell Ontology)
 
6)  Applications of the CL (Cell Ontology)
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 +
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''Agreed that there should be some group discussion of plant cells before this meeting.Laurel and Ramona will review the Cell Ontology.''
  
  
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Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).
 
Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).
 +
 +
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''Dennis can make June 30th, but Alejandra cannot travel that day -- can attend via conference call.''
  
  
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  Laurel and Ramona are preparing a short paper (up to 1 page) for submission to to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. Abstract/short paper submission deadline 4/16/10
 
  Laurel and Ramona are preparing a short paper (up to 1 page) for submission to to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. Abstract/short paper submission deadline 4/16/10
 +
 +
''Paper will be send around for comments this afternoon, to be submitted by the 15th.''
  
  
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*a maximum of 500 words to describe the scientific content.  
 
*a maximum of 500 words to describe the scientific content.  
 +
 +
 +
''Dennis is presenting in another symposium, but is not an organizer, so can organize an ontology symposium but not present. Some discussion of who presenters should be --  maybe Pankaj, Laurel and Ramona, Barry or Chris, someone from another plant-based ontology - perhaps Rex or Rosemary.  Dennis and Ramona will work on a draft proposal for next week's meeting''
  
  

Latest revision as of 20:41, 15 April 2010

POC meeting, Webex Conference Call; Date: April 13th, 2010 10am (PDT)

Minutes are in italics below each agenda item.


In attendance: POC members: Laurel Cooper (OSU),Alejandra Gandolfo, (Cornell University), Ramona Walls(NYBG), Dennis Stevenson (NYBG),

Collaborators: Rex Nelson-Soybase, USDA-ARS, Ames, Iowa

Absent: Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)


Agenda:

Acceptance of the minutes from last weeks meeting? All in favor?

Minutes accepted without changes.


Item carried over from last week's agenda:


1. Complete discussion of whorls:

a. whorled plant structure: definition: A collective plant structure composed of one or more whorls. (See SF Tracker: whorled plant structure).

Alejandra, Dennis, and Ramona felt strongly that 'androecium' and 'gynoecium' were phyllome whorls, along with the agreement of Laurel and Rex. Laurel discussed this again with Pankaj (after the call) and he agreed that since carpel and stamen are listed as phyllomes, that it makes sense to list androecium and gynoecium as phyllome whorls. So we all agreed to eliminate the term whorled plant structure, because it was redundant with 'whorled phyllome structure'.


b. Phyllome whorl:(See SF Tracker: whorled phyllome structure) Proposed def'n: "A collective plant structure that contains phyllomes arranged around a common node."

This was renamed as 'whorled phyllome structure'.

After the meeting Lol and Ramona proposed the new def'n: 'whorled phyllome structure': A collective plant structure that contains one or more whorled arrangements of phyllomes.

Children are androecium, calyx, corolla, epicalyx, gynoecium, leaf whorl, perianth and whorled tepal structure (new term, see below).


Note: Whorls that have been reduced to a single organ will be placed under 'plant organ'.


c. Proposed new term: tepal whorled structure: a whorled structure composed of two (four?) or more tepals. (See SF Tracker whorled tepal structure)


Agreed to rename the term whorled tepal structure. There was some discussion about whether or not this term should be a child of perianth.

After the meeting Lol and Ramona proposed the new def'n: 'whorled tepal structure': A whorled phyllome structure that is composed of two or more tepals


Also worked on definition of tepal(See SF Tracker: tepal)

proposed definition: A phyllome that is part of a perianth in which all parts are similar in appearance.


There was a discussion about cases in which petals, sepal, or tepals are arranged spirally, rather than in a whorl, as in basal dicots. This creates a problem for dealing with terms like perianth, which is usually whorled but may be a spiral. No solution was reached.

(See SF Tracker phyllome arrangement)


Items #2 and #3 were tabled for next week's discussion:

2. fruit (See SF Tracker: fruit)

Is a fruit an organ?

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.


proposed change: fruit is_a 'collective plant structure' and part_of infructescence. (CPS: a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue).



3. Embryo (See SF Tracker: embryo) Def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

-has no is_a parent, propose making it is_a whole plant?



4. Question from Laurel and Ramona about changing the references in OE when we rewrite the definitions of the terms (eg from MaizeGDB/TAIR to POC Curators). What is the correct protocol for doing this?

The people present concurred that if we are making a substantial rewrite of the definition, then the Dbxref should be changed to POC: curators. The ID number shows the history of who created the term. After the call, Pankaj pointed out that a substantial change in the definition would require a new ID#.


5. Upcoming Conferences and Meetings: Updates

  • Cell Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME. Laurel and Ramona will attend.

Scientific agenda will include:

1) Review and discussion of the ongoing work on specific areas of the Cell Ontology

2) Resolution of issues regarding the high level structure of the Cell Ontology

3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms

4) Organization of outreach efforts to import cell type terms from other ontologies and resources

5) Discussion about software enhancements to the AmiGO tool to enable and search of GO annotations that involve coannotation to CL terms

6) Applications of the CL (Cell Ontology)


Agreed that there should be some group discussion of plant cells before this meeting.Laurel and Ramona will review the Cell Ontology.


  • POC meeting/Annotation workshop to be held in Corvallis on June 30th. Ramona will be in Portland June 26-29.

Dennis is interested in also coming out, what about Barry, Chris and Alejandra?

Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).


Dennis can make June 30th, but Alejandra cannot travel that day -- can attend via conference call.


  • Bio-Ontologies 2010: Semantic Applications in Life Sciences. July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona may be going. Registration deadline May 28th, $325.

-Flash updates, up to 1 page: (short talks (5 min) giving the salient new developments on existing public ontologies) -Poster abstracts, up to 1 page (posters will be up for 2 days, with at least 1 poster session) Poster authors can also do a flash update. 

Laurel and Ramona are preparing a short paper (up to 1 page) for submission to to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. Abstract/short paper submission deadline 4/16/10

Paper will be send around for comments this afternoon, to be submitted by the 15th.


* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, mini symposium presentation. Abstract submitted 3/12/10.

Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene has been tentatively approved for Sunday Aug 1, 8am-12pm. more details TBA

  • Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island. Ramona presenting, Dennis attending, 15 minute oral presentation, Abstract submitted 3/26/10.


  • International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm): "Call of symposia closes" 3-31-10, Abstracts submission deadline: 12-1-10.

from 3-23-10: Dennis and Alejandra are planning to attend IBC2011. Dennis will work on possible symposium proposals. Pankaj can be co-organizer if necessary. Laurel and Ramona are interested in going if funds are available Alejandra and Ramona would check on the deadlines and Ramona will look into the req'ts for the symposium proposal. Updates?

Each symposium consists of six 20 minute sessions. Each person can give only one talk at the meeting, and can be an organizer for only one meeting. Each meeting must have two organizers. Speakers must cover their own travel costs. Organisers should emphasize broad international participation and appropriate gender balance. Symposium proposal consists of:

  • details of each proposed symposium including contact details of participants.
  • a maximum of 500 words to describe the scientific content.


Dennis is presenting in another symposium, but is not an organizer, so can organize an ontology symposium but not present. Some discussion of who presenters should be -- maybe Pankaj, Laurel and Ramona, Barry or Chris, someone from another plant-based ontology - perhaps Rex or Rosemary. Dennis and Ramona will work on a draft proposal for next week's meeting


from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.


  • Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.


8. Next meeting scheduled for Tuesday April 20th at 10am.

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