Planteome Ontology Development and Coordination Working Group: Difference between revisions

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=Participants=
=Participants=
* Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)
* 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)
* 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)
* CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)
** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),
** 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
* New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added
* Barry Smith, University at Buffalo (Ontology Consultant)
* Barry Smith, University at Buffalo (Ontology Consultant)
* Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added
* Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added
- Has left the project*
=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.
[[Ontology Working Group_Meetings- 2015]]
[[Ontology Working Group_Meetings- 2016]]
[[Ontology Working Group_Meetings- 2017]]
[[Jan 23rd, 2018 Ontology Working Group Meeting]]
[[Feb 27th, 2018 Ontology Working Group Meeting]]
[[March 16th, 2018 Ontology Meeting-Avocado + Cherimoya]]
[[April 10th, 2018 Ontology Working Group Meeting]]
[[April 13th, 2018 Plant Phenoscape Group Meeting]]
[[May 1st, 2018 Sanmita Demo]]
[[Oct. 30th, 2018 Web Site Refresh Meeting]]


=Goals and Objectives:=
=Goals and Objectives:=
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=Ontology Working Group Meetings:=
=Links to current versions of the Ontologies:=
Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)
[http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly
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]]
 
[[Ontology Working Group Meeting, Tuesday July 21st, 2015]]
 
[[Ontology Working Group Meeting, Aug 25th, 2015]]
 
[[Ontology Working Group Meeting, Sept 15th, 2015]]


=Links to current versions of the Ontologies:=
==Plant Trait Ontology (TO)==
==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:  
Link to most recent changes on GitHub:  
[https://github.com/Planteome/plant-trait-ontology  Plant Trait Ontology repository]
[https://github.com/Planteome/plant-trait-ontology  Plant Trait Ontology repository]

Latest revision as of 22:19, 31 October 2018

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), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)
    • 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

- Has left the project*

Ontology Working Group Meetings:

Ontology Working Group_Meetings- 2015

Ontology Working Group_Meetings- 2016

Ontology Working Group_Meetings- 2017

Jan 23rd, 2018 Ontology Working Group Meeting

Feb 27th, 2018 Ontology Working Group Meeting

March 16th, 2018 Ontology Meeting-Avocado + Cherimoya

April 10th, 2018 Ontology Working Group Meeting

April 13th, 2018 Plant Phenoscape Group Meeting

May 1st, 2018 Sanmita Demo

Oct. 30th, 2018 Web Site Refresh Meeting

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 Development Workshops

Planteome Curator workshop Fall 2015

Links to current versions of the Ontologies:

Planteome Development Browser Updates nightly

Plant Trait Ontology (TO)

Link to most recent changes on GitHub: Plant Trait Ontology repository

Plant Ontology (PO)

Crop Ontology (TO)

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