Difference between revisions of "POC Conf. Call 4-27-10"

From Plant Ontology Wiki
Jump to navigationJump to search
Line 98: Line 98:
  
  
 +
4. Upcoming Conferences and Meetings: Updates
  
−
'''Older items'''
+
    * Cell Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME. Laurel and Ramona will attend.
  
 +
Scientific agenda will include:
  
−
'''4. stem''' (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2982923&group_id=76834&atid=835555/ stem])
+
1) Review and discussion of the ongoing work on specific areas of the Cell Ontology
  
−
Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]
+
2) Resolution of issues regarding the high level structure of the Cell Ontology
  
−
Synonyms: cane, culm,  stalk, trunk
+
3) Relations to be employed and external ontologies to utilize in construction of logical definitions for cross-product terms
  
−
Problem: Stem has no is_a parent- should be a collective plant structure?
+
4) Organization of outreach efforts to import cell type terms from other ontologies and resources
  
−
OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.
+
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)
  
−
'''2. stalk''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972224&group_id=76834&atid=835555/ stalk])
 
  
−
This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.
+
Agreed that there should be some group discussion of plant cells before this meeting.Laurel and Ramona will review the Cell Ontology.
  
−
def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.
 
  
−
Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.
 
  
−
-made a cardinal organ part (as per its definition) rather than an organ.
 
  
−
'''Proposed children of stalk: (Test: do all of these fit the definition?)'''
+
    * POC meeting/Annotation workshop to be held in Corvallis on June 30th. Ramona will be in Portland June 26-29.
  
−
*filament: The stalk of a stamen.(stamen:organ)
+
Dennis can make June 30th, but Alejandra cannot travel that day -- can attend via conference call What about Barry and Chris?
  
−
*petiole: The stalk of a leaf. (leaf:organ)
+
Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).
  
−
*petiolule: The stalk of a leaflet (leaflet:cardinal organ part)
 
  
−
*funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)
+
Barry will be in France this week and can't attend. Pankaj suggested we plan on meeting for two days. Dennis has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th. Ramona will request that her talk be scheduled for the 27th or 28th.
  
−
*gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)
 
  
−
*leaf rachis: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ) (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972235&group_id=76834&atid=835555/ leaf rachis])
+
    * 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.  
  
−
*peduncle: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves. (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972231&group_id=76834&atid=835555/ peduncle])
+
-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.
  
−
propose revised def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).
+
Laurel submitted the 1 pager on Friday April 16th to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. We will be notified by May 7th if we are doing a flash update. Registration deadline May 28th, $325.
  
−
*pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]
 
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2975275&group_id=76834&atid=835555/ pedicel])
 
  
−
propose revised def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).
+
* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation. Abstract submitted 3/12/10 and workshop.
  
−
'''Note: We also have the term 'stem''''. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.
+
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.
  
−
'''3. More 'new is_a children of cardinal organ part''''  (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2971884&group_id=76834&atid=835555/ new is_a children of cardinal organ part])
+
Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. more details TBA
  
−
Several weeks ago, we created new children of cardinal organ part, from '''terms that had no is_a parent'''. We can deal with definitions and relationships of each term later, but for now we simply need to approve moving them to cardinal organ part.
+
    * International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):
  
−
Some of them can be dealt with later, but the terms listed here are a higher priority and/or can be dealt with very quickly. Many of the definitions need to be worked on at a future meeting. See Source Forge items for additional comments.
+
Dennis and Alejandra are planning to attend IBC2011. 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.
  
−
'''*receptacle:''' The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].
+
Updates?
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2975273&group_id=76834&atid=835555/ receptacle])
 
  
−
propose revised def'n: The region at the top of either the peduncle or pedicel where the floral appendages (for example, sepals, petals, stamens, and pistils) are attached.(Brooklyn Botanic Garden http://www.bbg.org/gar2/topics/botany/parts_flowers.html)
+
    * 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. Organizers should emphasize broad international participation and appropriate gender balance.  
  
−
Comments: If both pedicel and peduncle is_a stalk, and stalk is_a 'cardinal organ part', then both pedicel and peduncle must be part of some
+
Symposium proposal consists of:
−
organ for this to work.
 
−
 
−
'''*hypanthium'''- A cup- or tube-like structure bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary of a flower.
 
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972200&group_id=76834&atid=835555/ hypanthium])
 
  
−
made part_of receptacle instead of part_of flower
+
    * 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?
−
'''*pulvinus:'''-A more or less abrupt swelling, especially at the apex or base of a petiole or leaf sheath, often glandular and/or being the place where a plant responds to touch, gravity or light, in panicoid grasses a swollen region
 
−
in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary]
 
−
(See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972236&group_id=76834&atid=835555/ pulvinus])
 
−
 
 
−
-currently is_a (an) organ
 

Revision as of 16:21, 23 April 2010

POC meeting, Webex Conference Call; Date: April 27th, 2010 10am (PDT)

Agenda:

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


Items carried over from last week's agenda:


1. Collective phyllome structure and its children


A. collective phyllome structure (See SF tracker: collective phyllome structure).

Proposed def.:A collective plant structure that consists of two or more phyllomes originating on the stem from the same node or from two or more adjacent nodes with compressed internodes.

Unlike the definition we came up with last week, this definitions does not contain the undefined terms rosette and whorl. It also uses the term stem instead of axis, because stem is defined in the PO, and axis is not.


'Collective phyllome structure' would replace the term original term phyllome whorl (PO:0008033) which we have been calling 'whorled phyllome structure.' The proposed new term phyllome aggregation would be rejected.


'Whorl' and 'floral whorl' (a term used in GO) would be narrow synonyms.


Children (see items B and C below) are androecium, calyx, corolla, epicalyx, gynoecium, collective leaf structure, perianth, rosette, and collective tepal structure (new term proposed by Laurel and Pankaj after the meeting).


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


B. Children of collective phyllome structure: See SF tracker item new defintions for children of collective phyllome structure and item C below.


>>Androecium: A collective phyllome structure composed of two or more stamens.

>>Calyx: A collective phyllome structure composed of two or more sepals.

>>Corolla: A collective phyllome structure composed of two or more petals.

>>Epicalyx: A collective phyllome structure composed of two or more phyllomes immediately outside the calyx.

>>Gynoecium: A collective phyllome structure composed of two or more carpels.

>>Collective leaf structure: A collective phyllome structure composed of two or more leaves. Rosette and leaf whorl are synonyms.

>>Perianth: A collective phyllome structure composed of two or more petals, sepals, or tepals.

>>Collective tepal aggregation: A perianth composed of two or more tepals (Child of perianth, see item C below).


The proposed children rosette and whorl would be rejected. Rosette and leaf whorl would be synonyms of 'collective leaf structure' and whorl would be a synonym of 'collective phyllome structure'.


C. New term: collective tepal structure: (See SF Tracker collective tepal structure)

proposed new def'n: A perianth composed of two or more tepals.

is_a perianth


D. tepal (See SF Tracker: tepal)

proposed revised def'n: A phyllome that is part of a perianth in which all parts are similar in appearance and are neither petals nor sepals.


Check out the link to images for tepals on the dev browser: tepal

What do folks think of this as a way to include images in the PO? Is there a way to include images in the obo file?



2. fruit (See SF Tracker: fruit)

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

proposed definition (modified slightly from Gleason and Cronquist 2nd edition, via Dennis): A collective plant structure that contains a ripened ovary, together with any other structures that ripen with it and form a unit with it.


Does everyone agree that a fruit is a collective plant structure?

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?

-embryo contained_in archegonium could work for all land plants (maybe not charophytes), rather than contained_in seed (doi: 10.1111/j.1469-8137.2009.03054.x)


4. 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 can make June 30th, but Alejandra cannot travel that day -- can attend via conference call What about Barry and Chris?

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


Barry will be in France this week and can't attend. Pankaj suggested we plan on meeting for two days. Dennis has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th. Ramona will request that her talk be scheduled for the 27th or 28th. 


   * 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.

-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 submitted the 1 pager on Friday April 16th to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. We will be notified by May 7th if we are doing a flash update. Registration deadline May 28th, $325.


  • American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation. Abstract submitted 3/12/10 and workshop.

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 is scheduled for Saturday July 31, 8am-12pm. more details TBA 

   * International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):

Dennis and Alejandra are planning to attend IBC2011. 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. Organizers 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?

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-27-10&oldid=814"