Planteome.org - User contributions [en]

Nov 15th, 2016 Ontology Working Group Meeting

2016-11-14T21:33:12Z

Meiera: /* Open discussion about High Throughput Phenotyping */

=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:
* Regrets:

* Recordings:

==Agenda==
===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
* http://www.plant-phenomics.ac.uk/en/who-we-are/staff/john/

** 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===
* A number of Fruit types have recently been added to the PO

===Follow up from IC-FOODS Conference November 7-9, 2016 Davis, California- PJ and Mal attended===

= Upcoming Meetings and Workshops=
== 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/
* MAL will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Nov 15th, 2016 Ontology Working Group Meeting

2016-11-14T21:32:07Z

Meiera: /* Open discussion about High Throughput Phenotyping */

=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:
* Regrets:

* Recordings:

==Agenda==
===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
* http://www.plant-phenomics.ac.uk/en/who-we-are/staff/john/

** 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===
* A number of Fruit types have recently been added to the PO

===Follow up from IC-FOODS Conference November 7-9, 2016 Davis, California- PJ and Mal attended===

= Upcoming Meetings and Workshops=
== 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/
* MAL will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Nov 15th, 2016 Ontology Working Group Meeting

2016-11-14T19:11:46Z

Meiera: /* Planteome Ontology WG Zoom Meeting */

=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/103123769

* Attendees:
* Regrets:

* Recordings:

==Agenda==
===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
* http://www.plant-phenomics.ac.uk/en/who-we-are/staff/john/

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

=== Fruit types in the Plant Ontology===
* A number of Fruit types have recently been added to the PO:

===Follow up from IC-FOODS Conference November 7-9, 2016 Davis, California- PJ and Mal attended===

= Upcoming Meetings and Workshops=
== 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/
* MAL will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Nov 15th, 2016 Ontology Working Group Meeting

2016-10-25T20:17:41Z

Meiera: /* Planteome Ontology WG Zoom Meeting */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Nov 8th, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/103123769

* Attendees:
* Regrets:

* Recordings:

==Agenda==

'''will be updating over the next few weeks.'''

* First 30 minutes will be a presentation from John Doonan's group about their high-throughput phenotyping work.

* Questions (Time permitting)

* Open discussion about HTP and 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)!

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9, 2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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 is October 28, 2016

== 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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Nov 15th, 2016 Ontology Working Group Meeting

2016-10-25T19:58:22Z

Meiera: /* Agenda */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Nov 8th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/103123769

* Attendees:
* Regrets:

* Recordings:

==Agenda==

'''will be updating over the next few weeks.'''

* First 30 minutes will be a presentation from John Doonan's group about their high-throughput phenotyping work.

* Questions (Time permitting)

* Open discussion about HTP and 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)!

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9, 2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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 is October 28, 2016

== 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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Nov 15th, 2016 Ontology Working Group Meeting

2016-10-25T19:57:51Z

Meiera: /* Agenda */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Nov 8th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/103123769

* Attendees:
* Regrets:

* Recordings:

==Agenda==

'''will be updating over the next few weeks.'''

- First 30 minutes will be a presentation from John Doonan's group about their high-throughput phenotyping work.

- Questions (Time permitting)

- Open discussion about HTP and 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)!

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9, 2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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 is October 28, 2016

== 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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Nov 15th, 2016 Ontology Working Group Meeting

2016-10-25T19:57:32Z

Meiera: /* Agenda */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Nov 8th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/103123769

* Attendees:
* Regrets:

* Recordings:

==Agenda==

'''will be updating over the next few weeks.'''

- First 30 minutes will be a presentation from John Doonan's group about their high-throughput phenotyping work.
- Questions (Time permitting)
- Open discussion about HTP and 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)!

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9, 2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==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 is October 28, 2016

== 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
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]

==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** 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.

* 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

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

May 24th, 2016 Ontology Working Group Meeting

2016-05-23T23:26:53Z

Meiera: /* 1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday May. 24th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/400883197

* attendees:

=Agenda=
==1. Update from [http://tinyurl.com/ho4j922 PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France]==

* Planteome members attending: LC, MAL, AM, EA, GG, JD

* Reports from the meeting:
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home or http://tinyurl.com/hzsho6v

* About 70+ Participants attended: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"

* Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster

* Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"

* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

* Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
** Feedback on the TD template

* Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
** '' 9 participants, 7 crop species:''
***Nordine El- Hassouni - CIRAD - rice
***Trushar Shah- IITA, Kenya - cassava, cowpea, and banana
***Jeffery Detras - IRRI - rice
***Reinhard Simon - Centro Internacional de la Papa (CIP), Peru - potato/sweet potato
***Manuel Riuz - CIRAD, France / CIAT, Colombia - rice
*** Cecile Grenier - CIRAD/CIAT Colombia - rice
***Ashley DuVal - Mars, Inc USA - cacao
***Anthony Bolger - RWTH Aachen University - Institute for Biology 1, Germany
***Astrid Junker - IPK Gatersleben, Germany - HTP phenotyping
** '' Outcomes: ''
***No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
****the work is never truly "automated" -
****everything requires a human checkpoint.
***reference ontology space makes it very difficult to standardize workflow
****no one is an expert on all things we attempt to capture
****collaborating with other application ontologies or working groups is necessary
***High throughput phenotyping requires an entirely new standard vocabulary
****perhaps could be captured with a new set of "methods"?
****Only a few measurements are taken
****most of the "traits" are calculations and inferences

==2. Planning for ICBO/BioCreative Conference==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]

==3. Planning for Post-ICBO Curator Workshop ==
* The idea is this would be similar to the one held at OSU in November 2015

* Dates??
* Who is interested in attending ?
* Should we send out a survey?

* If people come for the week of ICBO, are they able to stay for an additional 5 days to a week?

* Other options: Perhaps do in September before OSU starts?

= Upcoming Meetings and Workshops=
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

May 24th, 2016 Ontology Working Group Meeting

2016-05-23T23:26:02Z

Meiera: /* 1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday May. 24th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/400883197

* attendees:

=Agenda=
==1. Update from [http://tinyurl.com/ho4j922 PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France]==

* Planteome members attending: LC, MAL, AM, EA, GG, JD

* Reports from the meeting:
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home or http://tinyurl.com/hzsho6v

* About 70+ Participants attended: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"

* Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster

* Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"

* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

* Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
** Feedback on the TD template

* Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
** '' 9 participants, 7 crop species:''
***Nordine El- Hassouni - rice
***Trushar Shah- IITA, Kenya - cassava, cowpea, and banana
***Jeffery Detras - IRRI - rice
***Reinhard Simon - Centro Internacional de la Papa (CIP), Peru - potato/sweet potato
***Manuel Riuz - CIRAD, France / CIAT, Colombia - rice
*** Cecile Grenier - CIRAD/CIAT Colombia - rice
***Ashley DuVal - Mars, Inc USA - cacao
***Anthony Bolger - RWTH Aachen University - Institute for Biology 1, Germany
***Astrid Junker - IPK Gatersleben, Germany - HTP phenotyping
** '' Outcomes: ''
***No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
****the work is never truly "automated" -
****everything requires a human checkpoint.
***reference ontology space makes it very difficult to standardize workflow
****no one is an expert on all things we attempt to capture
****collaborating with other application ontologies or working groups is necessary
***High throughput phenotyping requires an entirely new standard vocabulary
****perhaps could be captured with a new set of "methods"?
****Only a few measurements are taken
****most of the "traits" are calculations and inferences

==2. Planning for ICBO/BioCreative Conference==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]

==3. Planning for Post-ICBO Curator Workshop ==
* The idea is this would be similar to the one held at OSU in November 2015

* Dates??
* Who is interested in attending ?
* Should we send out a survey?

* If people come for the week of ICBO, are they able to stay for an additional 5 days to a week?

* Other options: Perhaps do in September before OSU starts?

= Upcoming Meetings and Workshops=
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

May 24th, 2016 Ontology Working Group Meeting

2016-05-23T22:52:31Z

Meiera: /* 1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday May. 24th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:
=Agenda=
==1. Update from [http://tinyurl.com/ho4j922 PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France]==

* Planteome members attending: LC, MAL, AM, EA, GG, JD

* Reports from the meeting:
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home or http://tinyurl.com/hzsho6v

* About 70+ Participants attended: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"

* Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster

* Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"

* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

* Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
** Feedback on the TD template

* Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
** '' 9 participants''
**7 crop species:
***rice
***cassava
***cowpea
***banana
***potato
***sweet potato
***cacao
** '' Outcomes: ''
***No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
****the work is never truly "automated" -
****everything requires a human checkpoint.
***reference ontology space makes it very difficult to standardize workflow
****no one is an expert on all things we attempt to capture
****collaborating with other application ontologies or working groups is necessary
***High throughput phenotyping requires an entirely new standard vocabulary
****perhaps could be captured with a new set of "methods"?
****Only a few measurements are taken
****most of the "traits" are calculations and inferences

==2. Planning for ICBO/BioCreative Conference==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]

==3. Planning for Post-ICBO Curator Workshop ==
* The idea is this would be similar to the one held at OSU in November 2015

* Dates??
* Who is interested in attending ?
* Should we send out a survey?

* If people come for the week of ICBO, are they able to stay for an additional week?

= Upcoming Meetings and Workshops=
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

May 24th, 2016 Ontology Working Group Meeting

2016-05-23T22:51:28Z

Meiera: /* 1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday May. 24th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:
=Agenda=
==1. Update from [http://tinyurl.com/ho4j922 PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France]==

* Planteome members attending: LC, MAL, AM, EA, GG, JD

* Reports from the meeting:
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home or http://tinyurl.com/hzsho6v

* About 70+ Participants attended: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"

* Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster

* Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"

* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

* Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
** Feedback on the TD template

* Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
** '' 9 participants''
**rice
**cassava
**cowpea
**banana
**potato
**sweet potato
**cacao
** '' Outcomes: ''
***No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
****the work is never truly "automated" -
****everything requires a human checkpoint.
***reference ontology space makes it very difficult to standardize workflow
****no one is an expert on all things we attempt to capture
****collaborating with other application ontologies or working groups is necessary
***High throughput phenotyping requires an entirely new standard vocabulary
****perhaps could be captured with a new set of "methods"?
****Only a few measurements are taken
****most of the "traits" are calculations and inferences

==2. Planning for ICBO/BioCreative Conference==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]

==3. Planning for Post-ICBO Curator Workshop ==
* The idea is this would be similar to the one held at OSU in November 2015

* Dates??
* Who is interested in attending ?
* Should we send out a survey?

* If people come for the week of ICBO, are they able to stay for an additional week?

= Upcoming Meetings and Workshops=
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

May 24th, 2016 Ontology Working Group Meeting

2016-05-23T22:50:09Z

Meiera: /* 1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday May. 24th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:
=Agenda=
==1. Update from [http://tinyurl.com/ho4j922 PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France]==

* Planteome members attending: LC, MAL, AM, EA, GG, JD

* Reports from the meeting:
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home or http://tinyurl.com/hzsho6v

* About 70+ Participants attended: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon: oral presentation (10 mins) LC: "The Planteome Project"

* Monday late afternoon: Poster presentation- LC, AM, MAL: Planteome Poster

* Tuesday morning: oral presentation (10 min)- AM: "Annotating germplasm using the Plant Trait Ontology in Planteome"

* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

* Tuesday afternoon: Hands-on Session (2.5 hours)- LV:
** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
** Feedback on the TD template

* Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop
** '' 9 participants''
**
** '' Outcomes: ''
***No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.
****the work is never truly "automated" -
****everything requires a human checkpoint.
***reference ontology space makes it very difficult to standardize workflow
****no one is an expert on all things we attempt to capture
****collaborating with other application ontologies or working groups is necessary
***High throughput phenotyping requires an entirely new standard vocabulary
****perhaps could be captured with a new set of "methods"?
****Only a few measurements are taken
****most of the "traits" are calculations and inferences

==2. Planning for ICBO/BioCreative Conference==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]

==3. Planning for Post-ICBO Curator Workshop ==
* The idea is this would be similar to the one held at OSU in November 2015

* Dates??
* Who is interested in attending ?
* Should we send out a survey?

* If people come for the week of ICBO, are they able to stay for an additional week?

= Upcoming Meetings and Workshops=
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T17:33:35Z

Meiera: /* 5. AmiGO2 Update: */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.
**Follow ups:
***Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used
***PJ would like to set up a meeting with some of the possible collaborators
===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

===Tools of interest===
*PhenoPackets is a 'glorified GAF' that will allow for more complex capture of information
*AgroVoc - something that might be useful for PSO relationships and interactions
*GACS - AgroVoc plus NATL and CABT
**less complex
**includes AgroVoc

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]
**agenda still in flux, should be more final by end of the week.

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Tuesday morning: Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
* Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
* Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse
**Currently only relationships that pass annotations are displayed:
***is_a
***occurs_in
***regulates

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
* Elizabeth and George are going, EA will present Planteome as part of her talk

== Meeting in Montpellier, 9-13 May 2016 ==
Link to tentative agenda/website: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T17:32:07Z

Meiera: /* 2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016 */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.
**Follow ups:
***Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used
***PJ would like to set up a meeting with some of the possible collaborators
===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

===Tools of interest===
*PhenoPackets is a 'glorified GAF' that will allow for more complex capture of information
*AgroVoc - something that might be useful for PSO relationships and interactions
*GACS - AgroVoc plus NATL and CABT
**less complex
**includes AgroVoc

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]
**agenda still in flux, should be more final by end of the week.

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Tuesday morning: Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
* Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
* Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
* Elizabeth and George are going, EA will present Planteome as part of her talk

== Meeting in Montpellier, 9-13 May 2016 ==
Link to tentative agenda/website: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T17:31:14Z

Meiera: /* 1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.
**Follow ups:
***Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used
***PJ would like to set up a meeting with some of the possible collaborators
===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

===Tools of interest===
*PhenoPackets is a 'glorified GAF' that will allow for more complex capture of information
*AgroVoc - something that might be useful for PSO relationships and interactions
*GACS - AgroVoc plus NATL and CABT
**less complex
**includes AgroVoc

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Tuesday morning: Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
* Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
* Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
* Elizabeth and George are going, EA will present Planteome as part of her talk

== Meeting in Montpellier, 9-13 May 2016 ==
Link to tentative agenda/website: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T17:26:36Z

Meiera: /* 1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.
**Follow ups:
***Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used
***PJ would like to set up a meeting with some of the possible collaborators
===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Tuesday morning: Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
* Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
* Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
* Elizabeth and George are going, EA will present Planteome as part of her talk

== Meeting in Montpellier, 9-13 May 2016 ==
Link to tentative agenda/website: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 5th, 2016 Ontology Working Group Meeting

2016-04-06T22:35:32Z

Meiera: /* Progress on developing the rice annotation files from IRRI */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 6th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789
- attendees: AM, MAL, LC, PJ, JE, CM, BS

[[File:Ontology WG Meeting 4-6-16 video.mp4|thumbnail|Ontology WG Meeting 4-6-16 video]]

[[File:Ontology WG Meeting 4-6-16 audio.m4a|thumbnail|Ontology WG Meeting 4-6-16 audio]]

=Agenda=
==Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==

* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* Cannot put the tinyurl here...

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

===Agenda===
* Still finalizing the agenda, meeting weds, final version TBA
** https://docs.google.com/a/cgxchange.org/document/d/1rRVEu8X-E_a5tgTFYMrC10Ag-cGE0mqUf_yICrU26QY/edit?usp=sharing

* First day- Plenary sessions, tool demos
** GG will give an ontology 101 session
* Following days hands-on sessions

===Agronomy Ontology- Medha Devare and Celine Aubert===
* meta analysis across platforms for agronomic trials
* trials, variables, measurements, farming practices
* Modeled after traits in trait dictionaries- is it crop specific then?
* Goal is to develop it in Owl using protege- currently not available
* CM: should coordinate with the Food Ontology folks- they will be having a workshop at ICBO

== Progress on developing the rice annotation files from IRRI==
* Austin and Marie-Angelique
** Problems- linking to the GRIMS database or linking to Genesys
** Using the institute code in Geneysis might allow for direct links to accession numbers

* taxon is not showing up as it is not in our slim yet
* awnless is a type of awn color????

* add accession # to label

== ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is April 25th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

==AmiGO2 issues continued.. ==
* New version of AmiGO is in the works- you can preview it here: http://tomodachi.berkeleybop.org/amigo/landing

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed
** annotations by species

==Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Planning to do release soon- by end of this month

==Other Items- Tabled for next meeting==

* Presentation for Biocuration meeting- Marie-Angelique

* Progress on the development of the V. 5 trait dictionaries- Marie-Angelique and/or Leo

* OBA development- Chris Mungall- moved to April 26th

= Upcoming Meetings and Workshops=
==[https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL is going and will be presenting a talk
** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates]
** Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
* Elizabeth and George are going, EA will present Planteome as part of her talk

== Meeting in Montpellier, 9-13 May 2016 ==
Link to tentative agenda/website: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:31:23Z

Meiera: /* content/concentration/amount */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait ([https://en.wikipedia.org/wiki/Metabolite definition of 'metabolite' is sufficiently vague])
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

24 “concentration” terms

45 “content” terms

9 both

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the '''amount''' of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition

*The number of entities of this type that are part of another entity.

=== Options: ===

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Keeps the TO "measurement agnostic", in the reference ontology sense

*Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:28:22Z

Meiera: /* Revisions to the upper-level categories */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait ([https://en.wikipedia.org/wiki/Metabolite definition of 'metabolite' is sufficiently vague])
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]
Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition

*The number of entities of this type that are part of another entity.

=== Options: ===

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Keeps the TO "measurement agnostic", in the reference ontology sense

*Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:10:42Z

Meiera: /* Revisions to the biochemical trait TO:0000277 branch of the TO: */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]
Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition

*The number of entities of this type that are part of another entity.

=== Options: ===

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Keeps the TO "measurement agnostic", in the reference ontology sense

*Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:09:37Z

Meiera: /* Options: */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition

*The number of entities of this type that are part of another entity.

=== Options: ===

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Keeps the TO "measurement agnostic", in the reference ontology sense

*Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:09:13Z

Meiera: /* Options: */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition

*The number of entities of this type that are part of another entity.

=== Options: ===

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Keeps the TO measurement agnostic, in the reference ontology sense

*Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:08:05Z

Meiera: /* content/concentration/amount */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition

*The number of entities of this type that are part of another entity.

=== Options: ===

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Might be problematic due to changing definitions of terms with existing annotations (none found on planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T22:00:09Z

Meiera: /* Revisions to the upper-level categories */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

Current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

metabolite content branch to be divided further in parallel to ChEBI

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

*The number of entities of this type that are part of another entity.

Options:

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Might be problematic due to changing definitions of terms with existing annotations (none found on planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T21:57:55Z

Meiera: /* content/concentration/amount */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

*The number of entities of this type that are part of another entity.

Options:

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Might be problematic due to changing definitions of terms with existing annotations (none found on planteome browser)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T21:56:02Z

Meiera: /* content/concentration/amount */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

*The number of entities of this type that are part of another entity.

Options:

'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.

*Might be problematic due to changing definitions of terms with existing annotations (eg:)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T21:55:21Z

Meiera: /* content/concentration/amount */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

*The number of entities of this type that are part of another entity.

Options:

'''Merge content and concentration terms'''
*this would allow for an overall reduction of terms.

*Might be problematic due to changing definitions of terms with existing annotations (eg:)

'''Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)'''

*Results in an overall addition of terms

*Adds unnecessary parent to cases where both content and concentration terms don't exist

[[File:Content concentration amount.jpg]]

File:Biochemical branch TO.png

2016-01-20T21:49:59Z

Meiera:

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-20T21:49:32Z

Meiera: /* Revisions to the upper-level categories */

Planteome Ontology WG Zoom Meeting
* Date: Thursday Jan. 21st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
'''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

=Report on the PAG Workshop with CG Collaborators Monday Jan 11th=
- 29 attendees

= Revisions to the biochemical trait TO:0000277 branch of the TO:=

==Revisions to the upper-level categories==

[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]

Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]

current upper level terms:

*TO:0000283 biological process related trait
*TO:0000282 enzymatic activity and protein content related trait
*TO:0000281 metabolite content related trait
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability

Suggest reducing to:

*mineral and ion content trait
*metabolite content trait
*biological process trait

[[File:biochemical branch TO.png]]

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

*The number of entities of this type that are part of another entity.

Options:

*Merge content and concentration terms

*Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)
[[File:Content concentration amount.jpg]]

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-15T23:56:23Z

Meiera: /* content/concentration/amount */

=Planteome Ontology WG Zoom Meeting:=
Date: Tuesday Jan. 19th, 2015
Time: 8:15am PST (GMT-8)
* Connection details: '''Join from PC, Mac, Linux, iOS or Android: '''
* Attendees: TBA

* [[File:|thumb|]]
* [[File:|thumb| ]]

==Planning for PAG Workshop with CG Collaborators Monday Jan 11th==

== content/concentration/amount==

Biochemists definitions:

*concentration = amount/ VOLUME

*content = amount/MASS

PATO defs:

*‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.

*'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

*The number of entities of this type that are part of another entity.

Options:

*Merge content and concentration terms

*Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)
[[File:Content concentration amount.jpg]]

File:Content concentration amount.jpg

2016-01-15T23:54:55Z

Meiera:

Jan 21st, 2016 Ontology Working Group Meeting

2016-01-15T23:52:28Z

Meiera: /* Planteome Ontology WG Zoom Meeting: */

Sept 15th, 2015- Ontology Working Group Meeting

2015-09-15T16:37:55Z

Meiera:

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

* In attendance: LC, MAL, AM, PJ
* Regrets:
* [[09/15/15 Meeting minutes]]
=Agenda=

== 1. Upcoming Plant Ontology Release #21 ==
For more information: [[http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]]

* New association data developed from the Plant Phenotype Pilot Project paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato

* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015.
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

* Many updated Xrefs and links
* Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN

* Timeline- within the next 2 weeks

== 2. Plant Trait Ontology: ==
Questions from Barry about how to define the traits:

---> image of TO upper level with "anatomy and morphology traits":

Example child terms:
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
** Added Xrefs to: number (PATO:0001555); TO_GIT:157

* stem size (TO:0000954):A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).
** Added Xrefs to: size (PATO:0000117); TO_GIT:157
** Added narrow synonym: stalk size

Objection has been raised to: 'associated with' - BS: (a) it is vague (b) it will block reasoning

Suggestions:
* stem number =def. a trait of a plant which is the number of stems of the plant"
and so on for the other cases

* infructescence axis shape: An infructescence axis anatomy and morphology trait (TO:0000921) that describes the shape of the infructescence axis [or specify the 'of' further]

synonym: cob shape

http://obofoundry.github.io/

Vertebrate Trait Ontology:
http://www.berkeleybop.org/ontologies/vt.owl -- “related to”

Animal Trait Ontology:
http://147.99.159.184:8080/webprotege/#ATOL -- “related to”

id: RO:0000086
name: has_quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string

ossible solution using relations from RO:

ear shape (TO:0000964):
An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.

Added dXrefs: shape (PATO:0000052);

Example from BATTO:

[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

> Are there any traits which are not anatomy and morphology traits?

''there are 8 different branches in the TO, anatomy and morphology trait is just one.''

> the term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?

" Yes, I suppose it means 'or'. It is inclusive. 'anatomy trait or morphology trait' would be more correct."

> Is there a definition of 'anatomy trait'?

>Is there a definition of 'morphology trait'?

>Are they logically disjoint?

== 3. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products

== 4. Proposed Meeting in Corvallis early November- ==

Goals of the meeting: Strategic planning and ontology curation

Who should attend:
Medicago, soybean, legume

== 5. TermGenie Demo ==

Thursday Aug 20th, 2015

2015-08-20T16:36:26Z

Meiera:

=Agenda=
Topic: Planteome Project All Hands Meeting
Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)
Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

* Who: LC, MAL, PJ, AM
* Regrets:

* Link to recording- Video: TBA
* Link to recording- Audio: TBA
=Minutes=
8/20/15

- members
- AM, lol, JE, JP, PJ
- MAL
- GK
- CS
- EZ
- Pankaj announcements
- Nov-Dec workshop (corvallis)
- goal: not just ontology training (OWL/Protege)
- stay for a couple days (1 week total) for actual hands on
- get people actually comfortable in the system.
- bring in OSU coordinators to manage
- Sept 7th(ish) NSF meeting to re-up the grant
- needs photos #ToDo
- make sure all extra money is spent on the grant's fiscal year.
- Chris' update/demo of new AmiGO curation pathway.
"11am next wed"
- Next all hands: sept 24th (likely to change)

- LoL update:
- moved from SVN to Github
- all 4 of ours
- some Crop ontology (maize wheat, rice, casava)
- everyone needs github IDs for access to our project
"john and george still need"

- Maria Angelique
- Crop ontologies
- uploading the 12 ontologies
- mapping between crop ontologies, and ref. ontologies
- RTB dev meeting
- 3 days
- discussing NGS
- RTB with BTI will split the work
- converting spreadsheets to ontology, but they lack complex mapping
- Priority is mapping
- using an automated tool
- working with chris to develop a workflow
- MAL has tried tools, chris has tools, need to find out what tool works best.
- prospective mapping is better than reterospective mapping
- Pankaj: ideal goal is to have a tool available for the workflow
- goal is to map back to reference ontology
- power comes from the xproducts

- Justin Elser
- all files (minus SVN) are over on github
- AmiGO2.0
- Far FAR faster
- won't load any annotations
- found a workaround with an old version of OWLtools
"not ideal"
- GO doesn't have this issue
- Can ChrisS help?
- can't help until the beginning of Sept.
- if JE can't figure it out by sept, ChrisS can help
- Post issues to Github's issues tracker on the Planteome-amigo2 repository
- JE will have it up and down frequently, so be wary when you're 'testing' it.
- iPlant won't get looked at until it is working on the live version
- iPlant
- where are we going to put the association files?
- the association files are too big for Github
- they are cluttered within the SVN
- keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
- irods: iPlant's 'big iron' is a possibility
- In the long run, it makes more sense to keep annotation/association files on iPlant
- mirror the latest version from version control(SVN) over on iPlant for 'bulk download' options for end users.

- Justin Preese
- Main goal: getting a web module for people to segment images, and link those segments to ontology terms/metadata
- There are desktop programs/algorithms that work, they are moving them to the web as 'modules'
- TL;DR-Newer/better/shinier graph cuts
- putting a module on iPlant BisQue that allows you to segment an image, and annotate it with ontologies.
- Doing a test environment locally, will expand to testing groups that are larger
- working with two students from CompSci
- 1. C++ and Matlab under the hood
- 2. Matlab and python on the surface for UI

== A. General Comments and Updates:==
=== Introductions: ===
* Any new faces Updates on new hires:

== B. Update from Ontologies Working Group:==

== C. Update from IT group- Data Store, AmiGO2- Justin Elser==

=== Migration to github ===
*Seems to be mostly complete. Let me know if there are any more files to transfer with history.

=== AmiGO 2 ===
Fixed annotation loading issue (well, a workaround)
*Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development.

== D. Update from AISO/BisQue group- Justin Preece==

==E. Other Comments:==

==Next meeting Thursday Sept 24th, 2015==

Ontology Working Group Meeting, Tuesday July 21st, 2015

2015-07-21T16:30:08Z

Meiera:

'''Time: 8am PDT (GMT-7:00) Pacific Time (US and Canada)'''

* In attendance: LC, MAL, AM, EA

Austin's scatterbrain notes:

7/21/15

- Participants:
- maria-anjelique
- Elizabeth Arnaud
- Lol
- Austin
- Priority 1
- improving dictionaries with trait names, et cetera
- make sure the trait is mapped to the ontologies
- lentil, pidgeonpea, cowpea, 3 dictionaries need to upload
- OBO files generated computationally are intersection of trait and scale
- end of July: all trait dictionaries revised and sent to BIPP (no idea on this acronym)
"behind schedule, so 10 by end of aug."
- waiting on validation of variables, and structure.
"variables = how the trait is measured."
- MAL- working on the file and OBO structure
"still wanting to work on the mapping"
- Mapping will not be a separate file, it will be imbedded
- Needs to be validated first (the trait dictionary).
- some already on Github
- trait name, variable name, scale
- second priority:
"PDO"
- Disease ontology needs reviewed.
- plan for overall structure needs made (next week)
- Share google spreadsheet with us from the CO, done by french group
- need to unify a plan from the 3 ontologies
- Early August deadline
-
- OSU's targets
- look at stress traits in TO
- TO has been switched to Github
"no longer updating the SVN"
- Need to migrate the trackers
-
- migrate PO and EO
- identify overall plan for PDO pathogens
- unclear as what should be a synonym
- Migrate PDO
- JE- working with seth and chris to fix AmiGO2
- OWL conversion from OBO in process
- Upper level conversation
- what dictionaries become ontologies?
- Workshop planning
- PJ and EA need to figure out who is getting trained on OWL
- sessions for mapping? Or just ontology demo
- AM + MAL
- train for OWL
- Need to know when
- Austin
- Afula (sp?)
"cassava guy"
- only one still using OBO
- PAG meeting another option for OWL training
"not ideal"
- Teach someone OWL in 3 days? This is tough for people with little exposure
- need goals
- Clear goals will be key
- nama working with afula, and soon to CIP
- should ask her how far everyone she works with needs training in.
- Maybe just CIP and banana people need the training
- possible that no one needs to be upgraded
- Better to try and teach OWL, or just stick to teaching OBO
- if they are going to work in Planteome, OWL would be nice
- the endgame of each person should determine what should be taught (OBO or OWL)
- Background can decide what each person needs
- bioinformaticist- easy to learn programs, tougher to learn biology
- format
- trait dictionary
- excel
- ontology format?
- enriched relationships
- schedule:
- rice/wheat - still getting worked on
"end of July is the goal"
- rosemary and kate in charge of this
- Kate- working on the dictionary and data management
- rosemary is in charge of it
- Get George to join an ontology meeting
"also his postdoc"
- just get him in one of these meetings, and ask him about what he's doing, and find out if he can help us.
- been difficult because of everyone's schedule.
- Lets get a meeting going at PAG

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-23T16:00:09Z

Meiera: /* Updates on New Hires, etc */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/985703701

* Who will attend: LC, MAL, DWS, PJ, BS, AM
* Others: GG, JE ?
* Regrets: EA, CM

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* new [[Crop_Ontology_Pages]] on the wiki (MAL)
* Agrovoc discussion- Part of FAO
* Updates on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

== Updates on New Hires, etc==
* '''OSU: New Postdoc Curator has joined the team: Austin Meier'''
** Austin's Background:
***Born: Omaha, NE
***Undergraduate: BS biology (genetics): University of Iowa, Iowa City
***internship: Monsanto, Huxley IA
***Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

* NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging

==Report from Bioversity team: Marie_Angelique==

==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

===Test of a brand new algorithm developed at LASIGE in Lisbon===
*compound matching [http://ceur-ws.org/Vol-1317/om2014_poster2.pdf Poster]
*We ran first tests with TO-PO-PATO and COWheat-PO-PATO. The idea is to only look at the top results first to check if the things are ok. The top results were good for TO-PO-PATO. But we did not get result for COWheat-PO-PATO. Therefore we are working on that

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-23T15:59:53Z

Meiera: /* Updates on New Hires, etc */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/985703701

* Who will attend: LC, MAL, DWS, PJ, BS, AM
* Others: GG, JE ?
* Regrets: EA, CM

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* new [[Crop_Ontology_Pages]] on the wiki (MAL)
* Agrovoc discussion- Part of FAO
* Updates on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

== Updates on New Hires, etc==
* '''OSU: New Postdoc Curator has joined the team: Austin Meier'''
** Austin's Background:
***Born: Omaha, NE, 1986
***Undergraduate: BS biology (genetics): University of Iowa, Iowa City
***internship: Monsanto, Huxley IA
***Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

* NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging

==Report from Bioversity team: Marie_Angelique==

==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

===Test of a brand new algorithm developed at LASIGE in Lisbon===
*compound matching [http://ceur-ws.org/Vol-1317/om2014_poster2.pdf Poster]
*We ran first tests with TO-PO-PATO and COWheat-PO-PATO. The idea is to only look at the top results first to check if the things are ok. The top results were good for TO-PO-PATO. But we did not get result for COWheat-PO-PATO. Therefore we are working on that

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-23T15:59:15Z

Meiera: /* Updates on New Hires, etc */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/985703701

* Who will attend: LC, MAL, DWS, PJ, BS, AM
* Others: GG, JE ?
* Regrets: EA, CM

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* new [[Crop_Ontology_Pages]] on the wiki (MAL)
* Agrovoc discussion- Part of FAO
* Updates on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

== Updates on New Hires, etc==
* '''OSU: New Postdoc Curator has joined the team: Austin Meier'''
** Austin's Background:
Born: Omaha, NE, 1986
Undergraduate: BS biology (genetics): University of Iowa, Iowa City
internship: Monsanto, Huxley IA
Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

* NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging

==Report from Bioversity team: Marie_Angelique==

==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

===Test of a brand new algorithm developed at LASIGE in Lisbon===
*compound matching [http://ceur-ws.org/Vol-1317/om2014_poster2.pdf Poster]
*We ran first tests with TO-PO-PATO and COWheat-PO-PATO. The idea is to only look at the top results first to check if the things are ok. The top results were good for TO-PO-PATO. But we did not get result for COWheat-PO-PATO. Therefore we are working on that

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Planteome Ontology Development and Coordination Working Group

2015-06-23T15:53:11Z

Meiera: /* Participants */

=Participants=
* Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)
* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)
* CGIAR Consortium (Montpellier, France and CG centers around the world): '''Elizabeth Arnaud''' (Co-PI, Crop Ontology), '''Léo Valette''' (Curator, IBP + CO), Marie Angelique Laporte (Ontology Engineer)
** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),
* New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added
* Barry Smith, University at Buffalo (Ontology Consultant)
* Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added

=Goals and Objectives:=
==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==
The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images.

These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources.

The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.

* Plant Trait Ontology (TO)
* Plant Environment Ontology (EO)
* Plant Ontology (PO)
* Plant Stress Ontology (PSO)
* Coordination with the Phenotypic Qualities Ontology (PATO)
* Building references with the Crop Ontology (CO) as a resource of concepts for cROP

==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==
===2.1 Collaborative approaches on ontology development and annotation:===
* Transition to OWL Format
* Introduction of Elk reasoner and Continuous Integration (CI) system
* Development of TermGenie tool for TO and PO
* Use of Inferred graph completion

===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===
GOstruct method

===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===
Details TBA

=Ontology Working Group Meetings:=
Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)
Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. I apologize if this time does not work for everyone.

[[Ontology Working Group_Meetings- Jan 2015]]

[[Ontology Working Group_Meetings- Feb 2015]]

[[Ontology Working Group March 6th 2015]]

[[Ontology Working Group Meeting Tuesday March 31st]]

[[Ontology Working Group GitHub Meeting, Tuesday April 3rd, 2015]]

[[Ontology Working Group Meeting, Tuesday April 7th, 2015]]

[[Ontology Working Group Meeting, Tuesday April 28th, 2015]]

[[Ontology Working Group Meeting, Tuesday May 12th, 2015]]

[[Ontology Working Group Meeting, Tuesday May 26th, 2015]]

[[Ontology Working Group Meeting, Tuesday June 9th, 2015]]

[[Ontology Working Group Meeting, Tuesday June 23rd, 2015]]

=Links to current versions of the Ontologies:=
==Plant Trait Ontology (TO)==
[http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/browse.cgi?session_id=1852amigo1337966110 TO+PSO -Dev Browser] Updates nightly

[http://crop-dev.cgrb.oregonstate.edu/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=6933amigo1423596135 TO-Dev on Planteome Browser] * Not up to date...

Link to most recent changes on GitHub:
[https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]

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==Plant Ontology (PO)==

==Crop Ontology (TO)==
* [[Crop Ontology Pages]] on wiki
* Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]

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=Ontology Development Resources and Workshops=

TBA....

Planteome Ontology Development and Coordination Working Group

2015-06-22T22:55:01Z

Meiera:

=Participants=
* Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (curator)
* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)
* CGIAR Consortium (Montpellier, France and CG centers around the world): '''Elizabeth Arnaud''' (Co-PI, Crop Ontology), '''Léo Valette''' (Curator, IBP + CO), Marie Angelique Laporte (Ontology Engineer)
** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),
* New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added
* Barry Smith, University at Buffalo (Ontology Consultant)
* Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added

=Goals and Objectives:=
==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==
The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images.

These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources.

The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.

* Plant Trait Ontology (TO)
* Plant Environment Ontology (EO)
* Plant Ontology (PO)
* Plant Stress Ontology (PSO)
* Coordination with the Phenotypic Qualities Ontology (PATO)
* Building references with the Crop Ontology (CO) as a resource of concepts for cROP

==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==
===2.1 Collaborative approaches on ontology development and annotation:===
* Transition to OWL Format
* Introduction of Elk reasoner and Continuous Integration (CI) system
* Development of TermGenie tool for TO and PO
* Use of Inferred graph completion

===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===
GOstruct method

===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===
Details TBA

=Ontology Working Group Meetings:=
Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)
Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. I apologize if this time does not work for everyone.

[[Ontology Working Group_Meetings- Jan 2015]]

[[Ontology Working Group_Meetings- Feb 2015]]

[[Ontology Working Group March 6th 2015]]

[[Ontology Working Group Meeting Tuesday March 31st]]

[[Ontology Working Group GitHub Meeting, Tuesday April 3rd, 2015]]

[[Ontology Working Group Meeting, Tuesday April 7th, 2015]]

[[Ontology Working Group Meeting, Tuesday April 28th, 2015]]

[[Ontology Working Group Meeting, Tuesday May 12th, 2015]]

[[Ontology Working Group Meeting, Tuesday May 26th, 2015]]

[[Ontology Working Group Meeting, Tuesday June 9th, 2015]]

[[Ontology Working Group Meeting, Tuesday June 23rd, 2015]]

=Links to current versions of the Ontologies:=
==Plant Trait Ontology (TO)==
[http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/browse.cgi?session_id=1852amigo1337966110 TO+PSO -Dev Browser] Updates nightly

[http://crop-dev.cgrb.oregonstate.edu/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=6933amigo1423596135 TO-Dev on Planteome Browser] * Not up to date...

Link to most recent changes on GitHub:
[https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]

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==Plant Ontology (PO)==

==Crop Ontology (TO)==
* [[Crop Ontology Pages]] on wiki
* Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]

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=Ontology Development Resources and Workshops=

TBA....

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-22T22:44:29Z

Meiera: