Difference between revisions of "POC Conf. Call 5-4-10"

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POC Conf. Call 5-4-10
+
POC meeting, Webex Conference Call; Date: May 4th, 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)''
 +
 
 +
Collaborators: Rex Nelson-SOYbase, USDA-ARS, Ames, Iowa, Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico,
  
 +
''Absent: Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)''
  
−
POC meeting, Webex Conference Call; Date: May 4th, 2010 10am (PDT)
 
  
 
== Agenda: ==
 
== Agenda: ==
Line 8: Line 14:
  
 
Acceptance of the minutes from last weeks meeting? All in favor?
 
Acceptance of the minutes from last weeks meeting? All in favor?
 +
''There were no additions, deletions or changes to last weeks minutes.''
 +
 +
 +
'''Items carried over from last week's agenda:'''
 +
 +
 +
'''1. Wrapping up the phyllome structures that include 'whorls' and 'rosettes':'''
 +
 +
'''collective phyllome structure''' (See SF tracker: [http://sourceforge.net/tracker/?func=detail&aid=2980171&group_id=76834&atid=835555/ collective phyllome structure]).
 +
 +
New proposed def'n.:A collective plant structure that consists of two or more phyllomes originating from the same node or from two or more adjacent nodes with compressed internodes.
 +
 +
 +
This def'n avoids the use of the term 'stem' here. 'Whorl' and 'floral whorl' (a term used in GO) are narrow synonyms.
 +
 +
''This definition was approved by all present. The item will be accepted and closed on Source Forge.''
 +
 +
 +
'''2. fruit''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2972169&group_id=76834&atid=835555/ fruit])
 +
 +
Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.
 +
 +
Proposed def'n: A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it.
 +
 +
PJ (via SourceForge) offered a proposed def'n using 'post-fertilization'.
 +
 +
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).
 +
 +
 +
''POC conf call: Proposed new def'n:''
 +
''A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it.''
 +
''(Comment: exception parthenocarpy or other hormone-induced condition)''
 +
 +
''Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it).''
 +
 +
 +
 +
 +
 +
'''3.  Embryo''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555/ embryo])
 +
 +
'''Current def'n:''' A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]
 +
 +
 +
'''Proposed def'n:''' A young sporophyte before the period of rapid growth. [source: Raven et al.]
 +
 +
'''Comments:''' (1) In seed plants, germination marks the end of the embryonic phase.
 +
 +
(2) See [http://plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0000010&session_id=3880b1272975931/ Cultured embryo PO:0000010] for definition of in vitro plant embryo
 +
 +
(3) Adventitious embryos do not arise from zygotes
 +
 +
 +
Relationships:
 +
 +
(1) has no is_a parent, propose making it is_a whole plant?
 +
 +
(2) develops_from zygote (see comment above)
 +
 +
(3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)
 +
 +
 +
''Parentage: Those present agreed that it might be better to have embryo is_a sporphyte, which makes it a whole plant through transitivity.  Usually develops_from zygote''
 +
 +
''Also agreed that the phrase 'before the period of rapid growth' is too vague.''
 +
 +
POC Conf call: A young sporophyte before the period of rapid growth.
 +
 +
''This term will remain open as the def'n needs further refinement.''
 +
 +
 +
 +
 +
'''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)
  
−
Items carried over from last week's agenda:
 
  
 +
'''For group discussion:'''
  
 +
-Plant cell child terms: organization, completeness, definitions. Are we happy with them, or do we plan on a major overhaul?
  
 +
-- [http://plantontology.org/amigo/go.cgi?action=minus_node&search_constraint=terms&query=PO:0000423&session_id=5918b1272559194 PO browser with all cell types expanded]
  
 +
- List of PO plant cell types that are not in the Cell.obo file (thanks Rex!). Do we want to request that these terms be included in the CL?
  
 +
- Need to think about tissues and organs that we and CL might want to use for cross-product definitions.
  
−
'''Older items'''
+
- Should we aim for complete redundancy between cells in PO and plant cells in CL?
  
−
'''1. stem''' (See SF Tracker [https://sourceforge.net/tracker/?func=detail&aid=2982923&group_id=76834&atid=835555/ stem])
 
  
−
Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]
+
''Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting.  Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.''
  
−
Synonyms: cane, culm, stalk, trunk
+
''The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.''
  
−
Problem: Stem has no is_a parent- should be a collective plant structure?
+
''In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.''
  
−
OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.
+
''Laurel and/or Ramona will give a 10-15 minute presentation at the Cell Ontology meeting.''
  
  
−
'''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.
+
'''* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.'''
  
−
def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.
+
Pankaj suggested we plan on meeting for two days. Dennis can make June 30th, but has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th.
  
−
Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.
+
Alejandra cannot travel that day -- can attend via conference call.
  
−
-made a cardinal organ part (as per its definition) rather than an organ.
+
Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th.
 +
''Ramona has sent a request to schedule her talk on the 27th or 28th.''
 +
Barry will be in France this week and can't attend.
 +
What about Chris?
  
−
'''Proposed children of stalk: (Test: do all of these fit the definition?)'''
+
Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).
  
−
*filament: The stalk of a stamen.(stamen:organ)
 
  
−
*petiole: The stalk of a leaf. (leaf:organ)
+
'''* 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 are registered.
  
−
*petiolule: The stalk of a leaflet (leaflet:cardinal organ part)
+
-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.
  
−
*funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)
+
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.  
  
−
*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])
+
'''* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada.''' Laurel, Pankaj going,
 +
PO Poster presentation and Annotation Workshop with Gramene.
  
−
*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])
+
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.
  
−
propose revised def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).
+
We should prepare a brochure to distribute, similar to the one Gramene has.
  
−
*pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]
+
Annotation workshop with Gramene is scheduled for '''Saturday July 31, 8am-12pm'''. more details TBA
−
(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).
 
  
−
'''Note: We also have the term 'stem''''. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.
+
'''* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia'''. Important dates (http://www.ibc2011.com/Dates.htm):
  
 +
Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.
  
−
'''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])
+
Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with internet for outreach activities.  
  
−
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.
+
Pankaj will be co-organizer with Ramona. Laurel and Ramona are interested in going and speaking if funds are available.
  
−
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.
+
Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.
  
−
'''*receptacle:''' The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].
 
−
(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)
+
* '''Latin American Congress of Botany''' (http://www.botanica-alb.org/X_Congreso/index.php). La Serena, Chile, October 4-10; MAG: "I am not sure about due dates for this one due to the earthquake".
  
−
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
+
from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.
−
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
 
  
 +
* Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.
  
−
'''*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
+
'''8. Next meeting scheduled for Tuesday May 11th at 10am PDT.'''

Latest revision as of 21:18, 4 May 2010

POC meeting, Webex Conference Call; Date: May 4th, 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)

Collaborators: Rex Nelson-SOYbase, USDA-ARS, Ames, Iowa, Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico,

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


Agenda:

Acceptance of the minutes from last weeks meeting? All in favor? There were no additions, deletions or changes to last weeks minutes.


Items carried over from last week's agenda:


1. Wrapping up the phyllome structures that include 'whorls' and 'rosettes':

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

New proposed def'n.:A collective plant structure that consists of two or more phyllomes originating from the same node or from two or more adjacent nodes with compressed internodes.


This def'n avoids the use of the term 'stem' here. 'Whorl' and 'floral whorl' (a term used in GO) are narrow synonyms.

This definition was approved by all present. The item will be accepted and closed on Source Forge.


2. fruit (See SF Tracker: fruit)

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

Proposed def'n: A collective plant structure that contains a mature gynoecium, together with any other structures that ripen with it and form a unit with it.

PJ (via SourceForge) offered a proposed def'n using 'post-fertilization'.

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).


POC conf call: Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: exception parthenocarpy or other hormone-induced condition)

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it).



3. Embryo (See SF Tracker: embryo)

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]


Proposed def'n: A young sporophyte before the period of rapid growth. [source: Raven et al.]

Comments: (1) In seed plants, germination marks the end of the embryonic phase.

(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes


Relationships:

(1) has no is_a parent, propose making it is_a whole plant?

(2) develops_from zygote (see comment above)

(3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)


Parentage: Those present agreed that it might be better to have embryo is_a sporphyte, which makes it a whole plant through transitivity. Usually develops_from zygote

Also agreed that the phrase 'before the period of rapid growth' is too vague.

POC Conf call: A young sporophyte before the period of rapid growth.

This term will remain open as the def'n needs further refinement.



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)


For group discussion:

-Plant cell child terms: organization, completeness, definitions. Are we happy with them, or do we plan on a major overhaul?

-- PO browser with all cell types expanded

- List of PO plant cell types that are not in the Cell.obo file (thanks Rex!). Do we want to request that these terms be included in the CL?

- Need to think about tissues and organs that we and CL might want to use for cross-product definitions.

- Should we aim for complete redundancy between cells in PO and plant cells in CL?


Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting. Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.

The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.

In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.

Laurel and/or Ramona will give a 10-15 minute presentation at the Cell Ontology meeting.


* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.

Pankaj suggested we plan on meeting for two days. Dennis can make June 30th, but has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th.

Alejandra cannot travel that day -- can attend via conference call.

Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th. Ramona has sent a request to schedule her talk on the 27th or 28th. Barry will be in France this week and can't attend. What about Chris?

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


* 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 are registered.

-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.


* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation and Annotation Workshop with Gramene.

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 already planning to attend IBC2011 and speak in other symposia.

Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with internet for outreach activities.

Pankaj will be co-organizer with Ramona. Laurel and Ramona are interested in going and speaking if funds are available.

Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.


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 May 11th at 10am PDT.

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