Ontology Working Group Meetings- Jan 2015 - Revision history

Cooperl: /* 6.. Round table discussion on collaboration for ontology development and data annotations & key questions from partners: */

2015-03-31T21:57:00Z

6.. Round table discussion on collaboration for ontology development and data annotations & key questions from partners:

← Older revision		Revision as of 21:57, 31 March 2015
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	==5. Description on how both projects will articulate and how it should start? Laurel Cooper and Elizabeth Arnaud==		==5. Description on how both projects will articulate and how it should start? Laurel Cooper and Elizabeth Arnaud==

	==6.. Round table discussion on collaboration for ontology development and data annotations & key questions from partners:==		==6. Round table discussion on collaboration for ontology development and data annotations & key questions from partners:==
	===Possible Use Cases: Alignment of CO with Ref Ontologies===		===Possible Use Cases: Alignment of CO with Ref Ontologies===
	* Maize (CIMMYT, USDA, Gramene) and Sorghum (ICRISAT)		* Maize (CIMMYT, USDA, Gramene) and Sorghum (ICRISAT)

Cooperl: /* 4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France */

2015-02-12T17:40:32Z

4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France

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 ==4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France==
 http://bioportal.lirmm.fr/ontologies
 =Planteome Ontology Working Group Meeting- Jan 22, 2015=

Cooperl: /* 4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France */

2015-02-10T19:44:05Z

4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France

← Older revision		Revision as of 19:44, 10 February 2015
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	==4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France==		==4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France==
	~~''Add links and details here''~~		http://bioportal.lirmm.fr/ontologies

	=Planteome Ontology Working Group Meeting- Jan 22, 2015=		=Planteome Ontology Working Group Meeting- Jan 22, 2015=

Cooperl: /* Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015 */

2015-02-08T04:32:11Z

Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015

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	=Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015=		=Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015=
	~~'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''~~
	Moderator: Rex Nelson		Moderator: Rex Nelson
	==1. Meeting Participants:==		==1. Meeting Participants:==
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	==4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France==		==4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France==
	''Add links and details here''		''Add links and details here''


	=Planteome Ontology Working Group Meeting- Jan 22, 2015=		=Planteome Ontology Working Group Meeting- Jan 22, 2015=

Cooperl at 04:30, 8 February 2015

2015-02-08T04:30:57Z

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 =Kick Off Meeting: Monday January 5th, 2015=
 Who: EA, LC and PJ
 '''Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.'''
@@ Line 38: / Line 36: @@
 '''5. Upcoming: Planteome-CO Coordination meeting at PAG Jan 12th'''
-==Planteome Ontology Working Group Meeting- Jan 22, 2015==
+=Planteome Ontology Working Group Meeting- Jan 22, 2015=
 Who: EA, LC and PJ

Cooperl at 04:28, 8 February 2015

2015-02-08T04:28:11Z

← Older revision		Revision as of 04:28, 8 February 2015
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	==Kick Off Meeting: Monday January 5th, 2015==		=Kick Off Meeting: Monday January 5th, 2015=

	Who: EA, LC and PJ		Who: EA, LC and PJ

Cooperl: /* Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015 */

2015-02-08T03:29:11Z

Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015

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	'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''		'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''

	==~~Planteome_Ontology_Working_Group_Meeting~~- Jan 22, 2015==		==Planteome Ontology Working Group Meeting- Jan 22, 2015==

	Who: EA, LC and PJ		Who: EA, LC and PJ

Cooperl at 03:28, 8 February 2015

2015-02-08T03:28:14Z

← Older revision	Revision as of 03:28, 8 February 2015
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		==Kick Off Meeting: Monday January 5th, 2015==

		Who: EA, LC and PJ

		'''Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.'''

		'''1. Progress and Updates on the Crop Ontology (http://www.cropontology.org/)'''
		* Annotation of phenotyping data through the IBP (https://www.integratedbreeding.net)
		* Ontology manager on https://www.integratedbreeding.net/
		* CO traits used to populate
		* 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

		'''2. Ontology development and serving to users:'''
		* 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

		'''3. Annotations and linking- vision of how the data is going to be shared'''
		* 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'''
		* APIs can be set up as we move forward

		'''5. Upcoming: Planteome-CO Coordination meeting at PAG Jan 12th'''


		'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''

		==Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015==

		Who: EA, LC and PJ
		Points of Discussion:

		1. Planteome wiki set up
		* will add EA and others on her team as needed..
		* Will be closed, will have to login to access

		2. Interaction with DivSeek.
		* Ruth Bastow is on the board and is interested in coordinating between the projects. DivSeek is a partnership, advisory board role may create COI?

		3. Scientific Advisory Board- will have info on the wiki- create page for Scientific Advisory Board
		* Oversight, annual report, meeting in person or online
		* advocates to community, users and funding agencies
		* possibly representative from CG centers such as RH, PK

		4. Prioritizing the CO vocabularies for cross referencing and curator training
		* Rice- IRRI is shorthanded right now, possible person is Berta Miro- associated with IRRI (Ajay Kohli)
		* Maize and wheat - CIMMYT- Rosemary; Project already underway with LC + Mary Schaeffer
		** WheatIS and WDIWG of the RDA- interested in using ontologies and setting standards
		* Soybean- USDA Rex Nelson
		* Potato - CIP Reinhard, Richard Finkers (also other solanaceae)

		5. Planning is starting for Ontology Workshop in the Spring
		* Owl training, etc
		* more details TBA as they develop

		6. Collaboration possibilities with PL, AV and CJ, from IRD in Montpellier
		* CJ will be in Stanford this spring, has money for a postdoc for a year which will go away without a project.
		* Southgreen platform, involvement with 3000 rice genomes project
		* Semantic integration

		''To-do: create page for Scientific Advisory Board, Ontology Workshop''

Cooperl: Cooperl moved page Planteome Ontology Working Group Meeting- Jan 22, 2015 to Ontology Working Group Meetings- Jan 2015

2015-02-08T03:26:46Z

Cooperl moved page Planteome Ontology Working Group Meeting- Jan 22, 2015 to Ontology Working Group Meetings- Jan 2015

← Older revision		Revision as of 03:26, 8 February 2015
(No difference)

Cooperl: Blanked the page

2015-02-08T03:20:27Z

Blanked the page

← Older revision		Revision as of 03:20, 8 February 2015
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	~~Who: EA, LC and PJ~~

	~~Points of Discussion:~~

	~~1. Planteome wiki set up~~
	* will add EA and others on her team as needed..
	* Will be closed, will have to login to access

	~~2. Interaction with DivSeek.~~
	* Ruth Bastow is on the board and is interested in coordinating between the projects. DivSeek is a partnership, advisory board role may create COI?

	~~3. Scientific Advisory Board- will have info on the wiki- create page for Scientific Advisory Board~~
	* Oversight, annual report, meeting in person or online
	* advocates to community, users and funding agencies
	* possibly representative from CG centers such as RH, PK

	~~4. Prioritizing the CO vocabularies for cross referencing and curator training~~
	* Rice- IRRI is shorthanded right now, possible person is Berta Miro- associated with IRRI (Ajay Kohli)
	* Maize and wheat - CIMMYT- Rosemary; Project already underway with LC + Mary Schaeffer
	** WheatIS and WDIWG of the RDA- interested in using ontologies and setting standards
	* Soybean- USDA Rex Nelson
	* Potato - CIP Reinhard, Richard Finkers (also other solanaceae)

	~~5. Planning is starting for Ontology Workshop in the Spring~~
	* Owl training, etc
	* more details TBA as they develop

	~~6. Collaboration possibilities with PL, AV and CJ, from IRD in Montpellier~~
	* CJ will be in Stanford this spring, has money for a postdoc for a year which will go away without a project.
	* Southgreen platform, involvement with 3000 rice genomes project
	* Semantic integration


	~~''To-do: create page for Scientific Advisory Board, Ontology Workshop''~~