Difference between revisions of "POC Conf. Call 2-19-13"

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POC meeting, Webex Conference Call; Date: Tuesday Feb 19th, 2013 10am PST/1pm EST
 
POC meeting, Webex Conference Call; Date: Tuesday Feb 19th, 2013 10am PST/1pm EST
  
 +
In attendance: ''Laurel Cooper (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU).''
 +
 +
Absent: '' Pankaj Jaiswal (OSU)''
  
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In attendance:
 
  
  
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For the terms I have recently added, I think the best solution is to change the definitions.  These include the most children of the shoot system development stage (new PO:0025527).  I think I will to have to go back and revise the others at some point so that they are consistent.
+
For the terms I have recently added, I think the best solution is to change the definitions.  These include most children of the shoot system development stage (new PO:0025527).  I think I will to have to go back and revise the others at some point so that they are consistent.
  
−
* '''shoot system development stage (new PO:0025527)''': A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).
+
[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3595703&group_id=76834 shoot system development stage]
  
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added relation: shoot system (PO:0009006) participates_in shoot system development stage
+
*Current def'n: '''shoot system development stage (new PO:0025527)''': A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).
  
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Proposed Revised def'n:
+
Current relation: shoot system (PO:0009006) participates_in shoot system development stage
−
* '''shoot system development stage (new PO:0025527)''': A plant structure development stage (PO:0009012) that begins with the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage or death.
 
  
 +
Revised relation: shoot system (PO:0009006): shoot system development stage has_participant shoot system
  
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Notes:
+
''This should be shoot system development stage has_participant shoot system since the shoot system can exist outside of the shoot system development stage''
  
−
''Need to revise the definition of the shoot system to include all meristems, not just the the shoot apical meristems.  Also we decided that the shoot system development stage begins with the development of the plant organs and ends when the plant undergoes senescence and or death.''
 
  
−
current def'n:
+
''What about the development of vegetative shoots??  Also we decided that the shoot system development stage begins with the development of the plant organs and ends when the plant undergoes senescence and or death.''
−
A collective plant organ structure (PO:0025007) that produces shoot apical meristems (PO:0020148) and the plant structures that arise from them.  
 
  
−
What about the development of vegetative shoots??
+
Proposed Revised def'n:
 +
* '''shoot system development stage (new PO:0025527)''': A plant structure development stage (PO:0009012) that begins with the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (sporophyte senescent stage) or death.
  
 +
Revised relation: shoot system (PO:0009006): shoot system development stage has_participant shoot system.
  
−
Revised relation:  shoot system (PO:0009006) shoot system development stage has_participant shoot system
 
  
−
This should be shoot system development stage has_participant shoot system. Can the shoot system ever exist outside of the shoot system development stage? yes
 
  
 +
Notes:
  
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[[File:shoot sytem development stages.jpg]]
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''Need to revise the definition of the [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3028469&group_id=76834 shoot system] to include all meristems in the shoot system, not just the the shoot apical meristems (axial and lateral as well).''
  
 +
current def'n:
 +
*'''shoot system (PO:0009006)''': A collective plant organ structure (PO:0025007) that produces '''shoot apical meristems (PO:0020148)''' and the plant structures that arise from them.
  
−
Also need to revise:
 
  
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*'''bud development stage (new PO:0025528):''' A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).  
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[[File:shoot sytem development stages.jpg]]
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added relations: bud (PO:0009006) participates_in bud development stage (PO:0025528).
 
−
 
 
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revised def'n:  A shoot system development stage (PO:0025527) that begins
 
−
 
 
−
 
 
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* '''reproductive shoot system development stage''' (new PO:0025530)
 
−
 
 
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Proposed def'n: A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
 
−
 
 
−
add relation:  reproductive shoot system (PO:0025082) participates_in reproductive shoot system development stage (PO:0025530).
 
−
 
 
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* '''flower development stage (PO:0007615)''':  A reproductive shoot system development stage (PO:0025530) that has as primary participant a flower (PO:0009046).
 
−
 
 
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already has a cross product flower is participant, needs to be revised for the new parent term.
 
−
 
 
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*'''inflorescence development stage (PO:0001083)'''
 
−
 
 
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current def'n: A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
 
−
 
 
−
added relation:  inflorescence (PO:0009049) participates_in reproductive shoot system development stage (PO:0025530)
 
−
 
 
−
All have DbxRef to OBO_SF_PO: 3595703
 
−
 
 
−
==[http://sourceforge.net/tracker/?func=detail&aid=3597966&group_id=76834&atid=835555 prothallial cell]==
 
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On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
 
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prothallial cell (PO:0025533):
 
  
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proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.
 
  
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''should add the PO id for microgametophyte (PO:0025280) to the definition''
+
The rest of the terms in this hierarchy have been moved back to the [[Items_for_future_meetings]] page
  
 +
=Image Annotations=
  
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For reference about prothallial cells in gmnosperms see:
 
  
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Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
 
  
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Available online: [http://babel.hathitrust.org/cgi/pt?id=mdp.39015052524801;seq=356;view=1up;num=340 Coulter + Chamberlain, 1910]
 
  
 
=Upcoming meetings and Presentations 2013:=
 
=Upcoming meetings and Presentations 2013:=
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==10th Extended Semantic Web Conference (ESWC) Montpellier, 26-30 May 2013==
+
==1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013==
 +
[http://semantic-biodiversity.mpl.ird.fr/ S4BIODIV]
 +
 
 +
[http://2013.eswc-conferences.org/join-participant-0/participant-eswc2013 Registration Information ESWC 2013] 
 +
 
 +
Early Registration deadline March 17th
  
−
[http://2013.eswc-conferences.org/ Extended Semantic Web Conference] Montpellier
+
Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.
  
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Location: Montpellier, 26-30 May 2013.
+
Held in parallel with the 10th [http://2013.eswc-conferences.org/ Extended Semantic Web Conference (ESWC 2013)]
  
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[http://bioinfo-prod.mpl.ird.fr/semantic-biodiversity/index.php?option=com_content&view=article&id=76&Itemid=86 Semantics for Biodiversity (S4BIODIV)]
+
Workshop dates: May 26-27, 2013
  
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Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.  
+
IMPORTANT DATES:
 +
* Pre-submission inquiry deadline: February 24, 2013 (Abstract up to 500 words)
 +
* Submission Deadline:            March 4, 2013 (may be a little flexible)
 +
* Notification:                    April 1, 2013
 +
* Camera ready:                    April 15, 2013.
  
  
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Paraphrased from email exchange with EA (Bioversity):
+
TOPICS:
 +
 +
Scientific themes of interest (include but are not limited to):
 +
* sustainable agriculture
 +
* plant
 +
* health and habitat
 +
* relationship between plant-pests/pathogens
 +
* usages of plants by community
 +
* biodiversity conservation
 +
* ecosystems services
 +
* quality of biodiversity data
  
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Ontologies will be part of the workshop discussion. The latest development sent by Justin on AISO also raised interest of the organizing committee. So, we would you like that the Plant Ontology team be represented in the scientific committee of our workshop.
 
  
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This is a very first draft of course but will provide you with the context, scientific objectives, and expected outputs. Would you accept in principle (if the workshop is accepted and funds raised) to join our committee and submit a a paper for a presentation and/or poster? Deadline will be March and April.
+
Informatics technologies of interest (include but are not limited to):
 +
* ontology applications
 +
* knowledge engineering
 +
* linked biodiversity data
 +
* remote sensors
 +
* mobile devices
 +
* vizualization tools
 +
* data mining
  
 
==MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013==
 
==MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013==
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The New York Botanical Garden & Fordham University
 
The New York Botanical Garden & Fordham University
 +
 +
 +
==ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013==
 +
4th International Conference on Biomedical Ontologies 2013 (ICBO2013)
 +
 +
Concordia University, Montreal, Quebec, July 7th - 9th 2013  [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/cfp.html call for papers]
 +
 +
The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.
 +
 +
The event is part of the [http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/ Semantic Trilogy 2013] featuring:
 +
 +
* International Conference on Biomedical Ontologies (ICBO 2013)
 +
* Canadian Semantic Web Symposium (CSWS 2013)
 +
* Data Integration in the Life Sciences (DILS 2013)
  
 
==Botanical Society Meeting July 27-31st New Orleans==
 
==Botanical Society Meeting July 27-31st New Orleans==

Latest revision as of 17:43, 22 February 2013

POC meeting, Webex Conference Call; Date: Tuesday Feb 19th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU).

Absent: Pankaj Jaiswal (OSU)


Defining the plant structure development stages

On last week's conf call Barry said we should not be defining the plant structure development stages as a stage that has as a primary participant a plant structure and also adding the has_participant (or participates_in) relation as well. That makes sense as it does seem to be somewhat circular,and if the definitions are ever formalized, then it would be redundant. The problem is that we already have a whole bunch of them defined this way, besides the new ones added for the shoot system.


Examples already in the Plant Ontology:

  • collective plant organ structure development stage (PO:0025338)
  • whole plant development stage (PO:0007033)
  • fruit development stage (PO:0001002) (currently no has_participant relation to fruit)
  • plant organ development stage (PO:0025339)
  • plant tissue development stage (PO:0025423)
  • seed development stage (PO:0001170)
  • trichome development stage (PO:0025368)
  • gametophyte development stage (PO:0028003)
  • sporophyte development stage (PO:0028002)


For the terms I have recently added, I think the best solution is to change the definitions. These include most children of the shoot system development stage (new PO:0025527). I think I will to have to go back and revise the others at some point so that they are consistent.

shoot system development stage

  • Current def'n: shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).

Current relation: shoot system (PO:0009006) participates_in shoot system development stage

Revised relation: shoot system (PO:0009006): shoot system development stage has_participant shoot system

This should be shoot system development stage has_participant shoot system since the shoot system can exist outside of the shoot system development stage


What about the development of vegetative shoots?? Also we decided that the shoot system development stage begins with the development of the plant organs and ends when the plant undergoes senescence and or death.

Proposed Revised def'n:

  • shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that begins with the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (sporophyte senescent stage) or death.

Revised relation: shoot system (PO:0009006): shoot system development stage has_participant shoot system.


Notes:

Need to revise the definition of the shoot system to include all meristems in the shoot system, not just the the shoot apical meristems (axial and lateral as well).

current def'n:

  • shoot system (PO:0009006): A collective plant organ structure (PO:0025007) that produces shoot apical meristems (PO:0020148) and the plant structures that arise from them.


Shoot sytem development stages.jpg


The rest of the terms in this hierarchy have been moved back to the Items_for_future_meetings page

Image Annotations

Upcoming meetings and Presentations 2013:

Phenotype Ontology RCN Annual Summit Meeting, Feb. 25th - 27th, 2013, Durham, NC

Phenotype Ontology RCN

The workshop and meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, from Monday morning, February 25 through Wednesday noon, February 27th (you would arrive Sunday evening).

Overall goals: To introduce and establish communication and collaboration among scientists from different research backgrounds. The two primary themes: The use of text mining phenotypes and representing behavior in ontologies.

For more information: please contact Paula Mabee (pmabee@usd.edu)

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for abstracts for posters is Jan 31st.


website and registration are now open: Biocuration 2013

PRO-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

Goals:

  1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
  2. To identify potentially fruitful applications which such enhanced coordination might bring
  3. To enhance the Protein Ontology treatment of plant-related proteins
  4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
  5. To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]


Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)

BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO


1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013

S4BIODIV

Registration Information ESWC 2013

Early Registration deadline March 17th

Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.

Held in parallel with the 10th Extended Semantic Web Conference (ESWC 2013)

Workshop dates: May 26-27, 2013

IMPORTANT DATES:

  • Pre-submission inquiry deadline: February 24, 2013 (Abstract up to 500 words)
  • Submission Deadline: March 4, 2013 (may be a little flexible)
  • Notification: April 1, 2013
  • Camera ready: April 15, 2013.


TOPICS:

Scientific themes of interest (include but are not limited to):

  • sustainable agriculture
  • plant
  • health and habitat
  • relationship between plant-pests/pathogens
  • usages of plants by community
  • biodiversity conservation
  • ecosystems services
  • quality of biodiversity data


Informatics technologies of interest (include but are not limited to):

  • ontology applications
  • knowledge engineering
  • linked biodiversity data
  • remote sensors
  • mobile devices
  • vizualization tools
  • data mining

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University


ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013

4th International Conference on Biomedical Ontologies 2013 (ICBO2013)

Concordia University, Montreal, Quebec, July 7th - 9th 2013 call for papers

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.

The event is part of the Semantic Trilogy 2013 featuring:

  • International Conference on Biomedical Ontologies (ICBO 2013)
  • Canadian Semantic Web Symposium (CSWS 2013)
  • Data Integration in the Life Sciences (DILS 2013)

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract

Next meeting scheduled for Tuesday, Feb 26th, 2013 at 10am Pacific/1pm Eastern

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