Planteome Ontology Development and Coordination Working Group: Difference between revisions

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= Kick Off Meeting: Monday January 5th, 2015 =
=Participants=
'''Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.'''
* 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


Who: EA, LC and PJ
- Has left the project*


'''1.  Progress and Updates on the Crop Ontology (http://www.cropontology.org/)'''
=Ontology Working Group Meetings:=
* Annotation of phenotyping data through the IBP (https://www.integratedbreeding.net)
* Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)
* Ontology manager on https://www.integratedbreeding.net/
* Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html.  
* CO traits used to populate
[[Ontology Working Group_Meetings- 2015]]
* Agtrials (http://www.agtrials.org/) on CIAT another source
* Involvement of ICRISAT
* Genebank accessions- done at some centers e.g. CP
* Traits may be in common, but also there is variation between crops
* CO provides community-specific vocabularies for integration of data annotations


[[Ontology Working Group_Meetings- 2016]]


'''2. Ontology development and serving to users:'''
[[Ontology Working Group_Meetings- 2017]]
* With NSF's investment, they have certain requirements- need to minimize the duplication of efforts
* Centralized location for the ontology repositories- can be served to various portals as needed- such as the CO webpage the users are familiar with
* Need reliable system of versioning for the ontologies- Are the CO ones versioned currently?
* Reference ontologies need to be updated and expanded:
** Core reference ontologies: PO, TO, GO, ENVO/EO, PATO, ChEBI
** CO- species-specific vocabularies, ontologies
* CO has a tailored helpdesk for the users- needs to be maintained


* TO Development - could be opened to editing through Term Genie
[[Jan 23rd, 2018 Ontology Working Group Meeting]]


[[Feb 27th, 2018 Ontology Working Group Meeting]]


'''3.  Annotations and linking- vision of how the data is going to be shared'''
[[March 16th, 2018 Ontology Meeting-Avocado + Cherimoya]]
* SKOS format, OBO, move towards using OWL- at least in the reference ontologies
* Relations
* Need to be able to query across ontologies
* Need to create cross links between the crop-specific ontologies and the reference ones
* Design pilot project- pick a select group to focus on- will discuss further


'''4.  Online resources web services, provide links to databases'''
[[April 10th, 2018 Ontology Working Group Meeting]]
* APIs can be set up as we move forward


5. Upcoming:
[[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:=
[http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly
 
==Plant Trait Ontology (TO)==
Link to most recent changes on GitHub:
[https://github.com/Planteome/plant-trait-ontology  Plant Trait Ontology repository]
----
 
==Plant Ontology (PO)==
 
==Crop Ontology (TO)==
* [[Crop Ontology Pages]] on wiki
* Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]

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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