Nov 15th, 2016 Ontology Working Group Meeting: Difference between revisions

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* Date: Tuesday Nov 15th, 2016
* Date: Tuesday Nov 15th, 2016
* Time: 8:15am PST (GMT-8)
* Time: 8:15am PST (GMT-8)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/103123769
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/236619766
   
   
* Attendees:  
* Attendees: JD, AM, PJ, LC, MAL, EA, BtSinn, DC, BS, CM
* Regrets:  
* Regrets: DWS, JE


* Recordings:
* Recordings:
** [[File:Ontology Working Group meeting audio 11-15-16.m4a|thumb|Ontology Working Group meeting audio 11-15-16]]
** [[File:Ontology Working Group meeting video 11-15-2016.mp4|thumb|Ontology Working Group meeting video 11-15-2016]]


==Agenda==
=Agenda=
===Presentation from John Doonan: High-throughput Phenotyping ===
==Presentation from John Doonan: High-throughput Phenotyping ==
* John H Doonan, Professor of Genetics, Director; [http://www.plant-phenomics.ac.uk/en/ National Plant Phenomics Centre], Aberystwyth University
* John H Doonan, Professor of Genetics, Director; [http://www.plant-phenomics.ac.uk/en/ National Plant Phenomics Centre], Aberystwyth University
* http://www.plant-phenomics.ac.uk/en/who-we-are/staff/john/
* http://www.plant-phenomics.ac.uk/en/who-we-are/staff/john/
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** Questions (Time permitting)
** Questions (Time permitting)


===Open discussion about High Throughput Phenotyping===
==Open discussion about High Throughput Phenotyping==
*  Computer vision-based plant traits and their possible inclusion in the Plant Trait Ontology
*  Computer vision-based plant traits and their possible inclusion in the Plant Trait Ontology
** If you have topics you would like to discuss, please send them my way (meiera@science.oregonstate.edu)
Example:


=== Fruit types in the Plant Ontology===
*Normalized Difference Vegetation Index NDVI (NIR-Red)/(NIR+Red)
* A number of Fruit types have recently been added to the PO:


*Green Normalized Difference Vegetation Index GNDVI (NIR-Green)/(NIR+Green)


Do these traits actually require novel trait classes in the TO?  Or are they simply a different method used to measure existing traits (like Leaf Area Index (TO:0012001), or leaf area duration (TO:0012010)


Traits like plant height are a little more clear, as there doesn't seem to be a difference in the trait, so much as the technology used to make the measurement (they use similar scales, such as millimeters ).


===Follow up from IC-FOODS Conference November 7-9, 2016 Davis, California- PJ and Mal attended===
 
* If you have topics you would like to discuss, please send them my way (meiera@science.oregonstate.edu)
 
==Fruit types in the Plant Ontology==
Tabled for next meeting.....


= Upcoming Meetings and Workshops=
= Upcoming Meetings and Workshops=
== International Conference on Statistics & Big Data Bioinformatics in Agricultural Research, ICRISAT, India, Nov 20-23rd, 2016==
== [http://isas70.icrisat.ac.in/ International Conference on Statistics & Big Data Bioinformatics in Agricultural Research], ICRISAT, India, Nov 20-23rd, 2016==
* International Crops Research Institute for the Semi-Arid Tropics- ICRISAT http://www.icrisat.org/
* International Crops Research Institute for the Semi-Arid Tropics- ICRISAT http://www.icrisat.org/
* MAL will attend
* MAL will attend
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* Early bird registration deadline: October 16, 2016
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/


==Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA==
==Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA==
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* Poster Abstracts Submission Deadline Extension to Nov. 14, 11:59 pm EDT
* Poster Abstracts Submission Deadline Extension to Nov. 14, 11:59 pm EDT
** Editing Deadline:  11/28/16
** Editing Deadline:  11/28/16


== Phenome 2017, Feb 10th to 14th, 2017==
== Phenome 2017, Feb 10th to 14th, 2017==
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* DWS will attend- evo devo presentation
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing
* CM will attend and present Planteome and pheno-BLASTing
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* '''To be considered for a talk you must submit your abstract by November 17, 2016'''
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]
* January 9, 2017: Final deadline for abstracts to be in the online program and conference mobile app
* Early bird registrations till Dec. 1st- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]


==Biocuration 2017, March 26-29, 2017==
==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* http://biocuration2017.org
* To be considered for a talk, abstracts must be submitted by January 13, 2017
* Abstract submission deadline for posters is February 17, 2017
* Biocuration 2017 will bring together hundreds of leading curation scientists, bioinformaticians, and developers from all over the world to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research.
* Call for Workshops:  
* Call for Workshops:  
** Submission deadline: November 11, 2016
** Submission deadline: November 11, 2016
** Submission email: biocuration2017@lists.stanford.edu
** Submission email: biocuration2017@lists.stanford.edu
* Biocuration 2017 will bring together hundreds of leading curation scientists, bioinformaticians, and developers from all over the world to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research.


* The purpose of a workshop is to provide an opportunity for participants from academia and industry to present and discuss novel ideas on current and emerging topics relevant to biocuration.  Workshops are an excellent forum for exploring emerging approaches and task areas, for bridging the gaps between the curation and technology subfields of biocuration, and for critiquing existing approaches. This is a great opportunity to discuss specific topics with so many colleagues and working scientists gathered in the same location.   
* The purpose of a workshop is to provide an opportunity for participants from academia and industry to present and discuss novel ideas on current and emerging topics relevant to biocuration.  Workshops are an excellent forum for exploring emerging approaches and task areas, for bridging the gaps between the curation and technology subfields of biocuration, and for critiquing existing approaches. This is a great opportunity to discuss specific topics with so many colleagues and working scientists gathered in the same location.   


* For the best opportunity for consideration, proposals should be received by November 11, 2016.  Please submit a short paragraph (or two) describing the following:
* For the best opportunity for consideration, proposals should be received by November 11, 2016.  Please submit a short paragraph (or two) describing the following:
* Proposed scope and main objective, and their relation to biocuration
* Proposed scope and main objective, and their relation to biocuration
* Brief discussion of why the topic is of particular interest at this time
* Brief discussion of why the topic is of particular interest at this time

Latest revision as of 21:04, 17 November 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Nov 15th, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/236619766
  • Attendees: JD, AM, PJ, LC, MAL, EA, BtSinn, DC, BS, CM
  • Regrets: DWS, JE

Agenda

Presentation from John Doonan: High-throughput Phenotyping

    • first 30 minutes
    • Questions (Time permitting)

Open discussion about High Throughput Phenotyping

  • Computer vision-based plant traits and their possible inclusion in the Plant Trait Ontology

Example:

  • Normalized Difference Vegetation Index NDVI (NIR-Red)/(NIR+Red)
  • Green Normalized Difference Vegetation Index GNDVI (NIR-Green)/(NIR+Green)

Do these traits actually require novel trait classes in the TO? Or are they simply a different method used to measure existing traits (like Leaf Area Index (TO:0012001), or leaf area duration (TO:0012010)

Traits like plant height are a little more clear, as there doesn't seem to be a difference in the trait, so much as the technology used to make the measurement (they use similar scales, such as millimeters ).


  • If you have topics you would like to discuss, please send them my way (meiera@science.oregonstate.edu)

Fruit types in the Plant Ontology

Tabled for next meeting.....

Upcoming Meetings and Workshops

International Conference on Statistics & Big Data Bioinformatics in Agricultural Research, ICRISAT, India, Nov 20-23rd, 2016

4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016

Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA

http://www.intlpag.org/

  • October 31 early registration deadline
  • Deadline for workshop abstract submissions is December 2, 2016.
  • Deadline for changes to program (posting speakers) is November 30, 2016
  • Poster Abstracts Submission Deadline Extension to Nov. 14, 11:59 pm EDT
    • Editing Deadline: 11/28/16

Phenome 2017, Feb 10th to 14th, 2017

http://www.phenome2017.org/#homepage

  • DWS will attend- evo devo presentation
  • CM will attend and present Planteome and pheno-BLASTing
  • To be considered for a talk you must submit your abstract by November 17, 2016
  • January 9, 2017: Final deadline for abstracts to be in the online program and conference mobile app
  • Early bird registrations till Dec. 1st- Registration Link

Biocuration 2017, March 26-29, 2017

  • To be considered for a talk, abstracts must be submitted by January 13, 2017
  • Abstract submission deadline for posters is February 17, 2017
  • Biocuration 2017 will bring together hundreds of leading curation scientists, bioinformaticians, and developers from all over the world to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research.
  • Call for Workshops:
    • Submission deadline: November 11, 2016
    • Submission email: biocuration2017@lists.stanford.edu
  • The purpose of a workshop is to provide an opportunity for participants from academia and industry to present and discuss novel ideas on current and emerging topics relevant to biocuration. Workshops are an excellent forum for exploring emerging approaches and task areas, for bridging the gaps between the curation and technology subfields of biocuration, and for critiquing existing approaches. This is a great opportunity to discuss specific topics with so many colleagues and working scientists gathered in the same location.
  • For the best opportunity for consideration, proposals should be received by November 11, 2016. Please submit a short paragraph (or two) describing the following:
  • Proposed scope and main objective, and their relation to biocuration
  • Brief discussion of why the topic is of particular interest at this time
  • Suggested format (talks, panel discussion, etc.)
  • Potential speakers, panels, or other activities

XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China

Workshop proposal accepted

ICBO 2017, Sept 12th-15th, 2017

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