Ontology Working Group Meetings- Feb 2015 - Revision history

Cooperl at 20:26, 20 April 2015

2015-04-20T20:26:04Z

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	'''* [[Ontology Working Group meeting: Tuesday, Feb 10th, 2015]]		'''* [[Ontology Working Group meeting: Tuesday, Feb 10th, 2015]]'''
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	'''* [[Ontology Working Group Meeting Tuesday, Feb 17th, 2015]]'''		'''* [[Ontology Working Group Meeting Tuesday, Feb 17th, 2015]]'''

Cooperl at 20:25, 20 April 2015

2015-04-20T20:25:44Z

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	'''* [[Ontology Working Group meeting: Tuesday, Feb 10th, 2015]]		'''* [[Ontology Working Group meeting: Tuesday, Feb 10th, 2015]]
	'''		'''
	* [[Ontology Working Group Meeting Tuesday, Feb 17th, 2015]]		'''* [[Ontology Working Group Meeting Tuesday, Feb 17th, 2015]]'''

	* [[Ontology Working Group Meeting Tuesday, Feb 24th, 2015]]		'''* [[Ontology Working Group Meeting Tuesday, Feb 24th, 2015]]'''

	Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page		Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Cooperl: Replaced content with "'''* Ontology Working Group meeting: Tuesday, Feb 10th, 2015 ''' * Ontology Working Group Meeting Tuesday, Feb 17th, 2015 * Ontology Working Group Meeting Tuesd..."

2015-04-20T20:24:49Z

Replaced content with "'''* Ontology Working Group meeting: Tuesday, Feb 10th, 2015 ''' * Ontology Working Group Meeting Tuesday, Feb 17th, 2015 * Ontology Working Group Meeting Tuesd..."

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Cooperl: /* Tuesday, Feb 10th, 2015 */

2015-04-20T20:20:45Z

Tuesday, Feb 10th, 2015

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	=Tuesday, Feb 10th, 2015=		[[Ontology Working Group meeting: Tuesday, Feb 10th, 2015]]
	~~Who: PJ, EA, LC, JE, CM, BS~~
	* Meetings will be held using Zoom (https://www.zoom.us/) - we are in the process of getting it set up
	* Wiki is set up and notes will be kept here, need to login to access

	~~== 1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc==~~
	~~PJ: Initial goal will be to work on improving and updating the TO~~

	~~EA provided an overview of the Crop Ontology curation tool (http://www.cropontology.org/) and some background information about the ontologies and platform.~~

	~~Long term goal is to integrate the CO vocabularies with the reference ontologies.~~
	* Part of the Integrated Breeding Platform
	* Common vocabularies are used to integrate data from breeders field book
	* Was started as part of the Generation Challenge Program (GCP), which has run out of funding. The GCP Pantheon webiste (http://pantheon.generationcp.org/index.php) will be shut down soon and so that information needs to be moved somewhere else. Could perhaps go the the [http://genesys.cgxchange.org/gcp-crop-ontology GCP Wiki] page?

	* 18 crops (http://www.cropontology.org/) represented in five sections:
	** General Germplasm Ontology
	** Phenotype and Trait Ontology
	** Structural and Functional Genomic Ontology
	** Location and Environmental Ontology
	** Plant Anatomy & Development Ontology

	~~Cassava Example: http://www.cropontology.org/ontology/CO_334/Cassava~~
	* Based on OBO-Edit
	* Excel-based template
	* Visualized by the tool

	~~Common Trait Classes (e.g.) : Maize Ontology (http://www.cropontology.org/ontology/CO_322/Maize)~~
	* "Agronomic/Agronomical"
	* Morphological
	* Stress (Abiotic/Biotic Stresses)
	* Phenological
	* Quality
	* Unit

	~~Relations:~~
	* is_a
	* part _of
	* method_of
	* scale _of
	* derived_from

	~~Availability and Formats:~~
	* Download from www.cropontology.org
	* API- http://www.cropontology.org/api
	* make 'Permalink' to individual terms pages
	* Formats include csv, OBO, SKOS, RDF, Trait Template v4
	* Ones in blue are OBO based
	* Terms are translated into various languages, as synonyms

	~~Terms have a unique identifier:~~
	* CO_###:#######

	~~===Questions and Discussion: ===~~
	* Goal is to keep the web-based tool for user access, in some form.
	* Database behind it is No-SQL based
	* Integration with future versions of Term Genie
	* We will need a technical call as we we move towards integration at GitHub
	* The Trait Ontology is not displayed here as it was confusing to the users.
	* Identified an issue where curators/users can upload an ontology without any quality control.

	~~==2. Prioritizing the work on the species-specific Crop Ontologies- Rice, Wheat and Maize==~~
	* At the PAG meeting- Rice, wheat and Maize were identified as the best candidates to start on
	* The PO is well set up to provide entity terms for these as they are important crop/model species
	* The TO has some of the needed terms, but will need additional work

	~~''Fill in some details of the Rice, Wheat and Maize vocabs here:''~~

	~~==3. Transition to GitHub Repository==~~
	~~[https://github.com/Planteome Planteome Ontologies on GitHub]~~
	* This will be very useful for editting and versioning, then the relased version can be pushed out to Crop Ontology site

	~~==4. Hiring at Bioversity, OSU and NYBG==~~
	* Bioversity Curator position is advertised on the [http://www.bioversityinternational.org/jobs/ Bioversity Jobs page]:
	~~You can view it here: [https://hr4u.bioversity.cgiar.org/recruitment/Attachments%5CVA_Post%20Doc_CropOntology_NSF_MPL_Final.pdf Position Description: Post Doctoral Fellow, Crop Ontology, MPL~~]

	* Ontology Curator Position at OSU: In progress....


	* Ontology Curator Position at NYBG: In progress....

	~~==5. Possible Ontology development workshop this spring==~~
	~~Time is quite short, maybe consider a web-conferencing strategy to start, new people are being added to project at OSU, NYBG, CO~~

	~~==6. White paper on plant phenotyping standards==~~
	~~See details on [http://wiki.planteome.org/index.php/Thursday_Feb_6th,_2015#F._Position_Paper_or_.22White_Paper.22 All Hands Call Feb 6th~~]


	=Tuesday, Feb 17th, 2015=		=Tuesday, Feb 17th, 2015=

Cooperl at 20:18, 20 April 2015

2015-04-20T20:18:23Z

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	[[Ontology Working Group Meeting Tuesday, Feb 24th, 2015]]		[[Ontology Working Group Meeting Tuesday, Feb 24th, 2015]]

			Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Cooperl: /* Tuesday, Feb 17th, 2015 */

2015-04-20T20:16:43Z

Tuesday, Feb 17th, 2015

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	''Plan is to eventually host these annotations at the Planteome to do more advanced searches, at least at the population level with associations with links to MaizeGDB where the bulk of the data will be stored. With QTLs and linkage disequilibrium''		''Plan is to eventually host these annotations at the Planteome to do more advanced searches, at least at the population level with associations with links to MaizeGDB where the bulk of the data will be stored. With QTLs and linkage disequilibrium''

			[[Ontology Working Group Meeting Tuesday, Feb 24th, 2015]]

Cooperl: /* Tuesday, Feb 24th, 2015 */

2015-04-20T20:15:03Z

Tuesday, Feb 24th, 2015

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	''Plan is to eventually host these annotations at the Planteome to do more advanced searches, at least at the population level with associations with links to MaizeGDB where the bulk of the data will be stored. With QTLs and linkage disequilibrium''		''Plan is to eventually host these annotations at the Planteome to do more advanced searches, at least at the population level with associations with links to MaizeGDB where the bulk of the data will be stored. With QTLs and linkage disequilibrium''

	~~=Tuesday, Feb 24th, 2015=~~
	~~Who: BS, LC, PJ, EA, DWS~~
	~~==1. Review of the Crop Ontology Structure==~~
	* Website: Crop Ontology Curation Tool http://www.cropontology.org/

	* CO Meeting March 2014: https://sites.google.com/a/cgxchange.org/cropontologycommunity/
	* [https://docs.google.com/viewer?a=v&pid=sites&srcid=Y2d4Y2hhbmdlLm9yZ3xjcm9wb250b2xvZ3ljb21tdW5pdHl8Z3g6M2E4OTU0ZDFhZDc1MDYyZQ Crop Ontology_Co & phenotyping - ARNAUD .pdf]

	* Rosemary Shrestha is the curator of the maize and wheat CO trait ontologies
	* Curators for the different ontologies are scattered around the world at the different CGIAR centers

	~~==2. United Nations Environmental Program adopts the OBO foundry ontologies==~~
	* Support of data collection for the sustainability goals
	* Building a framenwork
	* Crops are quite important

Cooperl: /* 2. United Nations Environmental Program adopts the OBO foundry ontologies */

2015-04-20T20:14:52Z

2. United Nations Environmental Program adopts the OBO foundry ontologies

← Older revision		Revision as of 20:14, 20 April 2015
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	* Curators for the different ontologies are scattered around the world at the different CGIAR centers		* Curators for the different ontologies are scattered around the world at the different CGIAR centers

	=2. United Nations Environmental Program adopts the OBO foundry ontologies=		==2. United Nations Environmental Program adopts the OBO foundry ontologies==
	* Support of data collection for the sustainability goals		* Support of data collection for the sustainability goals
	* Building a framenwork		* Building a framenwork
	* Crops are quite important		* Crops are quite important

Cooperl: /* 1. Review of the Crop Ontology Structure */

2015-04-20T20:14:41Z

1. Review of the Crop Ontology Structure

← Older revision		Revision as of 20:14, 20 April 2015
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	=Tuesday, Feb 24th, 2015=		=Tuesday, Feb 24th, 2015=
	Who: BS, LC, PJ, EA, DWS		Who: BS, LC, PJ, EA, DWS
	=1. Review of the Crop Ontology Structure=		==1. Review of the Crop Ontology Structure==
	* Website: Crop Ontology Curation Tool http://www.cropontology.org/		* Website: Crop Ontology Curation Tool http://www.cropontology.org/

Cooperl: /* 1. Review of the Crop Ontology Structure */

2015-03-16T16:44:29Z

1. Review of the Crop Ontology Structure

← Older revision		Revision as of 16:44, 16 March 2015
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	* Website: Crop Ontology Curation Tool http://www.cropontology.org/		* Website: Crop Ontology Curation Tool http://www.cropontology.org/

	CO Meeting March 2014: https://sites.google.com/a/cgxchange.org/cropontologycommunity/		* CO Meeting March 2014: https://sites.google.com/a/cgxchange.org/cropontologycommunity/
	* [https://docs.google.com/viewer?a=v&pid=sites&srcid=Y2d4Y2hhbmdlLm9yZ3xjcm9wb250b2xvZ3ljb21tdW5pdHl8Z3g6M2E4OTU0ZDFhZDc1MDYyZQ Crop Ontology_Co & phenotyping - ARNAUD .pdf]		* [https://docs.google.com/viewer?a=v&pid=sites&srcid=Y2d4Y2hhbmdlLm9yZ3xjcm9wb250b2xvZ3ljb21tdW5pdHl8Z3g6M2E4OTU0ZDFhZDc1MDYyZQ Crop Ontology_Co & phenotyping - ARNAUD .pdf]